Goals:
!curl http://histo.ucsf.edu/BMS270/BMS270_2018/code/cdt_reader.py > cdt_reader.py
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 3360 100 3360 0 0 100k 0 --:--:-- --:--:-- --:--:-- 102k
!ls *.py
cdt_reader.py stats.py
import cdt_reader
(colnames,genes,annotations,data) = cdt_reader.parse_cdt("supp2data.cdt")
(colnames,genes,annotations,data2) = cdt_reader.parse_cdt("supp2data.cdt",0.)
data[0][:10]
[None, None, 0.33, -0.17, 0.04, -0.07, -0.09, -0.12, -0.03, -0.2]
data2[0][:10]
[0.0, 0.0, 0.33, -0.17, 0.04, -0.07, -0.09, -0.12, -0.03, -0.2]
import cdt_reader
(colnames,genes,annotations,data) = cdt_reader.parse_cdt("supp2data.cdt")
data[0][:10]
[None, None, 0.33, -0.17, 0.04, -0.07, -0.09, -0.12, -0.03, -0.2]
import importlib
importlib.reload(cdt_reader)
(colnames,genes,annotations,data) = cdt_reader.parse_cdt("supp2data.cdt")
data[0][:10]
--------------------------------------------------------------------------- ValueError Traceback (most recent call last) /home/bms270/BMS270_2018/cdt_reader.py in parse_cdt(filename, null_value) 56 try: ---> 57 row_data.append(float(field)) 58 except ValueError: ValueError: could not convert string to float: 'YBR166C' During handling of the above exception, another exception occurred: AssertionError Traceback (most recent call last) <ipython-input-15-5afbb7cdbfed> in <module>() 1 importlib.reload(cdt_reader) ----> 2 (colnames,genes,annotations,data) = cdt_reader.parse_cdt("supp2data.cdt") 3 data[0][:10] /home/bms270/BMS270_2018/cdt_reader.py in parse_cdt(filename, null_value) 57 row_data.append(float(field)) 58 except ValueError: ---> 59 assert(field == "") 60 row_data.append(null_value) 61 AssertionError:
importlib.reload(cdt_reader)
(colnames,genes,annotations,data) = cdt_reader.parse_cdt("supp2data.cdt")
data[0][:10]
[0.33, -0.17, 0.04, -0.07, -0.09, -0.12, -0.03, -0.2, -0.06, -0.06]
dir()
['In', 'Out', '_', '_10', '_11', '_12', '_16', '_3', '__', '___', '__builtin__', '__builtins__', '__doc__', '__loader__', '__name__', '__package__', '__spec__', '_dh', '_exit_code', '_i', '_i1', '_i10', '_i11', '_i12', '_i13', '_i14', '_i15', '_i16', '_i17', '_i2', '_i3', '_i4', '_i5', '_i6', '_i7', '_i8', '_i9', '_ih', '_ii', '_iii', '_oh', '_sh', 'annotations', 'cdt_reader', 'colnames', 'data', 'data2', 'exit', 'genes', 'get_ipython', 'importlib', 'quit', 'urllib']
%who
annotations cdt_reader colnames data data2 genes importlib urllib
!man lsof
LSOF(8) System Manager's Manual LSOF(8)
NNAAMMEE
lsof - list open files
SSYYNNOOPPSSIISS
llssooff [ --??aabbCChhKKllnnNNOOPPRRttUUvvVVXX ] [ --AA _A ] [ --cc _c ] [ ++cc _c ] [ ++||--dd _d ] [
++||--DD _D ] [ ++||--ee _s ] [ ++||--EE ] [ ++||--ff [[ccffggGGnn]] ] [ --FF _[_f_] ] [ --gg _[_s_] ] [
--ii _[_i_] ] [ --kk _k ] [ ++||--LL _[_l_] ] [ ++||--mm _m ] [ ++||--MM ] [ --oo _[_o_] ] [ --pp _s ]
[ ++||--rr _[_t_[_m_<_f_m_t_>_]_] ] [ --ss _[_p_:_s_] ] [ --SS _[_t_] ] [ --TT _[_t_] ] [ --uu _s ] [ ++||--ww
] [ --xx _[_f_l_] ] [ --zz _[_z_] ] [ --ZZ _[_Z_] ] [ ---- ] [_n_a_m_e_s]
DDEESSCCRRIIPPTTIIOONN
_L_s_o_f revision 4.89 lists on its standard output file information about
files opened by processes for the following UNIX dialects:
Apple Darwin 9 and Mac OS X 10.[567]
FreeBSD 8.[234], 9.0, 10.0 and 11.0 for AMD64-based systems
Linux 2.1.72 and above for x86-based systems
Solaris 9, 10 and 11
(See the DDIISSTTRRIIBBUUTTIIOONN section of this manual page for information on
how to obtain the latest _l_s_o_f revision.)
An open file may be a regular file, a directory, a block special file,
a character special file, an executing text reference, a library, a
stream or a network file (Internet socket, NFS file or UNIX domain
socket.) A specific file or all the files in a file system may be
selected by path.
Instead of a formatted display, _l_s_o_f will produce output that can be
parsed by other programs. See the --FF, option description, and the OOUUTT‐‐
PPUUTT FFOORR OOTTHHEERR PPRROOGGRRAAMMSS section for more information.
In addition to producing a single output list, _l_s_o_f will run in repeat
mode. In repeat mode it will produce output, delay, then repeat the
output operation until stopped with an interrupt or quit signal. See
the ++||--rr _[_t_[_m_<_f_m_t_>_]_] option description for more information.
OOPPTTIIOONNSS
In the absence of any options, _l_s_o_f lists all open files belonging to
all active processes.
If any list request option is specified, other list requests must be
specifically requested - e.g., if --UU is specified for the listing of
UNIX socket files, NFS files won't be listed unless --NN is also speci‐
fied; or if a user list is specified with the --uu option, UNIX domain
socket files, belonging to users not in the list, won't be listed
unless the --UU option is also specified.
Normally list options that are specifically stated are ORed - i.e.,
specifying the --ii option without an address and the --uufoo option pro‐
duces a listing of all network files OR files belonging to processes
owned by user ``foo''. The exceptions are:
1) the `^' (negated) login name or user ID (UID), specified with the --uu
option;
2) the `^' (negated) process ID (PID), specified with the --pp option;
3) the `^' (negated) process group ID (PGID), specified with the --gg
option;
4) the `^' (negated) command, specified with the --cc option;
5) the (`^') negated TCP or UDP protocol state names, specified with
the --ss _[_p_:_s_] option.
Since they represent exclusions, they are applied without ORing or AND‐
ing and take effect before any other selection criteria are applied.
The --aa option may be used to AND the selections. For example, specify‐
ing --aa, --UU, and --uufoo produces a listing of only UNIX socket files that
belong to processes owned by user ``foo''.
Caution: the --aa option causes all list selection options to be ANDed;
it can't be used to cause ANDing of selected pairs of selection options
by placing it between them, even though its placement there is accept‐
able. Wherever --aa is placed, it causes the ANDing of all selection
options.
Items of the same selection set - command names, file descriptors, net‐
work addresses, process identifiers, user identifiers, zone names,
security contexts - are joined in a single ORed set and applied before
the result participates in ANDing. Thus, for example, specifying
--ii@aaa.bbb, --ii@ccc.ddd, --aa, and --uufff,ggg will select the listing of
files that belong to either login ``fff'' OR ``ggg'' AND have network
connections to either host aaa.bbb OR ccc.ddd.
Options may be grouped together following a single prefix -- e.g., the
option set ``--aa --bb --CC'' may be stated as --aabbCC. However, since values
are optional following ++||--ff, --FF, --gg, --ii, ++||--LL, --oo, ++||--rr, --ss, --SS, --TT, --xx
and --zz. when you have no values for them be careful that the following
character isn't ambiguous. For example, --FFnn might represent the --FF and
--nn options, or it might represent the nn field identifier character fol‐
lowing the --FF option. When ambiguity is possible, start a new option
with a `-' character - e.g., ``--FF --nn''. If the next option is a file
name, follow the possibly ambiguous option with ``--'' - e.g., ``--FF ----
_n_a_m_e''.
Either the `+' or the `-' prefix may be applied to a group of options.
Options that don't take on separate meanings for each prefix - e.g., --ii
- may be grouped under either prefix. Thus, for example, ``+M -i'' may
be stated as ``+Mi'' and the group means the same as the separate
options. Be careful of prefix grouping when one or more options in the
group does take on separate meanings under different prefixes - e.g.,
++||--MM; ``-iM'' is not the same request as ``-i +M''. When in doubt, use
separate options with appropriate prefixes.
--?? --hh These two equivalent options select a usage (help) output
list. _L_s_o_f displays a shortened form of this output when it
detects an error in the options supplied to it, after it has
displayed messages explaining each error. (Escape the `?'
character as your shell requires.)
--aa causes list selection options to be ANDed, as described above.
--AA _A is available on systems configured for AFS whose AFS kernel
code is implemented via dynamic modules. It allows the _l_s_o_f
user to specify _A as an alternate name list file where the
kernel addresses of the dynamic modules might be found. See
the _l_s_o_f FAQ (The FFAAQQ section gives its location.) for more
information about dynamic modules, their symbols, and how they
affect _l_s_o_f.
--bb causes _l_s_o_f to avoid kernel functions that might block -
_l_s_t_a_t(2), _r_e_a_d_l_i_n_k(2), and _s_t_a_t(2).
See the BBLLOOCCKKSS AANNDD TTIIMMEEOOUUTTSS and AAVVOOIIDDIINNGG KKEERRNNEELL BBLLOOCCKKSS sec‐
tions for information on using this option.
--cc _c selects the listing of files for processes executing the com‐
mand that begins with the characters of _c. Multiple commands
may be specified, using multiple --cc options. They are joined
in a single ORed set before participating in AND option selec‐
tion.
If _c begins with a `^', then the following characters specify
a command name whose processes are to be ignored (excluded.)
If _c begins and ends with a slash ('/'), the characters
between the slashes are interpreted as a regular expression.
Shell meta-characters in the regular expression must be quoted
to prevent their interpretation by the shell. The closing
slash may be followed by these modifiers:
b the regular expression is a basic one.
i ignore the case of letters.
x the regular expression is an extended one
(default).
See the _l_s_o_f FAQ (The FFAAQQ section gives its location.) for
more information on basic and extended regular expressions.
The simple command specification is tested first. If that
test fails, the command regular expression is applied. If the
simple command test succeeds, the command regular expression
test isn't made. This may result in ``no command found for
regex:'' messages when lsof's --VV option is specified.
++cc _w defines the maximum number of initial characters of the name,
supplied by the UNIX dialect, of the UNIX command associated
with a process to be printed in the COMMAND column. (The _l_s_o_f
default is nine.)
Note that many UNIX dialects do not supply all command name
characters to _l_s_o_f in the files and structures from which _l_s_o_f
obtains command name. Often dialects limit the number of
characters supplied in those sources. For example, Linux
2.4.27 and Solaris 9 both limit command name length to 16
characters.
If _w is zero ('0'), all command characters supplied to _l_s_o_f by
the UNIX dialect will be printed.
If _w is less than the length of the column title, ``COMMAND'',
it will be raised to that length.
--CC disables the reporting of any path name components from the
kernel's name cache. See the KKEERRNNEELL NNAAMMEE CCAACCHHEE section for
more information.
++dd _s causes _l_s_o_f to search for all open instances of directory _s
and the files and directories it contains at its top level.
++dd does NOT descend the directory tree, rooted at _s. The ++DD _D
option may be used to request a full-descent directory tree
search, rooted at directory _D.
Processing of the ++dd option does not follow symbolic links
within _s unless the --xx or --xx ll option is also specified. Nor
does it search for open files on file system mount points on
subdirectories of _s unless the --xx or --xx ff option is also
specified.
Note: the authority of the user of this option limits it to
searching for files that the user has permission to examine
with the system _s_t_a_t(2) function.
--dd _s specifies a list of file descriptors (FDs) to exclude from or
include in the output listing. The file descriptors are spec‐
ified in the comma-separated set _s - e.g., ``cwd,1,3'',
``^6,^2''. (There should be no spaces in the set.)
The list is an exclusion list if all entries of the set begin
with `^'. It is an inclusion list if no entry begins with
`^'. Mixed lists are not permitted.
A file descriptor number range may be in the set as long as
neither member is empty, both members are numbers, and the
ending member is larger than the starting one - e.g., ``0-7''
or ``3-10''. Ranges may be specified for exclusion if they
have the `^' prefix - e.g., ``^0-7'' excludes all file
descriptors 0 through 7.
Multiple file descriptor numbers are joined in a single ORed
set before participating in AND option selection.
When there are exclusion and inclusion members in the set,
_l_s_o_f reports them as errors and exits with a non-zero return
code.
See the description of File Descriptor (FD) output values in
the OOUUTTPPUUTT section for more information on file descriptor
names.
++DD _D causes _l_s_o_f to search for all open instances of directory _D
and all the files and directories it contains to its complete
depth.
Processing of the ++DD option does not follow symbolic links
within _D unless the --xx or --xx ll option is also specified. Nor
does it search for open files on file system mount points on
subdirectories of _D unless the --xx or --xx ff option is also
specified.
Note: the authority of the user of this option limits it to
searching for files that the user has permission to examine
with the system _s_t_a_t(2) function.
Further note: _l_s_o_f may process this option slowly and require
a large amount of dynamic memory to do it. This is because it
must descend the entire directory tree, rooted at _D, calling
_s_t_a_t(2) for each file and directory, building a list of all
the files it finds, and searching that list for a match with
every open file. When directory _D is large, these steps can
take a long time, so use this option prudently.
--DD _D directs _l_s_o_f_'_s use of the device cache file. The use of this
option is sometimes restricted. See the DDEEVVIICCEE CCAACCHHEE FFIILLEE
section and the sections that follow it for more information
on this option.
--DD must be followed by a function letter; the function letter
may optionally be followed by a path name. _L_s_o_f recognizes
these function letters:
?? - report device cache file paths
bb - build the device cache file
ii - ignore the device cache file
rr - read the device cache file
uu - read and update the device cache file
The bb, rr, and uu functions, accompanied by a path name, are
sometimes restricted. When these functions are restricted,
they will not appear in the description of the --DD option that
accompanies --hh or --?? option output. See the DDEEVVIICCEE CCAACCHHEE
FFIILLEE section and the sections that follow it for more informa‐
tion on these functions and when they're restricted.
The ?? function reports the read-only and write paths that
lsof can use for the device cache file, the names of any envi‐
ronment variables whose values _l_s_o_f will examine when forming
the device cache file path, and the format for the personal
device cache file path. (Escape the `?' character as your
shell requires.)
When available, the bb, rr, and uu functions may be followed by
the device cache file's path. The standard default is
_._l_s_o_f___h_o_s_t_n_a_m_e in the home directory of the real user ID that
executes _l_s_o_f, but this could have been changed when _l_s_o_f was
configured and compiled. (The output of the --hh and --??
options show the current default prefix - e.g., ``.lsof''.)
The suffix, _h_o_s_t_n_a_m_e, is the first component of the host's
name returned by _g_e_t_h_o_s_t_n_a_m_e(2).
When available, the bb function directs _l_s_o_f to build a new
device cache file at the default or specified path.
The ii function directs _l_s_o_f to ignore the default device cache
file and obtain its information about devices via direct calls
to the kernel.
The rr function directs _l_s_o_f to read the device cache at the
default or specified path, but prevents it from creating a new
device cache file when none exists or the existing one is
improperly structured. The rr function, when specified without
a path name, prevents _l_s_o_f from updating an incorrect or out‐
dated device cache file, or creating a new one in its place.
The rr function is always available when it is specified with‐
out a path name argument; it may be restricted by the permis‐
sions of the _l_s_o_f process.
When available, the uu function directs _l_s_o_f to read the device
cache file at the default or specified path, if possible, and
to rebuild it, if necessary. This is the default device cache
file function when no --DD option has been specified.
++||--ee _s exempts the file system whose path name is _s from being sub‐
jected to kernel function calls that might block. The ++ee
option exempts _s_t_a_t(2), _l_s_t_a_t(2) and most _r_e_a_d_l_i_n_k(2) kernel
function calls. The --ee option exempts only _s_t_a_t_(_2_) and
_l_s_t_a_t(2) kernel function calls. Multiple file systems may be
specified with separate ++||--ee specifications and each may have
_r_e_a_d_l_i_n_k(2) calls exempted or not.
This option is currently implemented only for Linux.
CCAAUUTTIIOONN:: this option can easily be mis-applied to other than
the file system of interest, because it uses path name rather
than the more reliable device and inode numbers. (Device and
inode numbers are acquired via the potentially blocking
_s_t_a_t(2) kernel call and are thus not available, but see the
++||--mm _m option as a possible alternative way to supply device
numbers.) UUssee tthhiiss ooppttiioonn wwiitthh ggrreeaatt ccaarree aanndd ffuullllyy ssppeecciiffyy
tthhee ppaatthh nnaammee ooff tthhee ffiillee ssyysstteemm ttoo bbee eexxeemmpptteedd..
When open files on exempted file systems are reported, it may
not be possible to obtain all their information. Therefore,
some information columns will be blank, the characters
``UNKN'' preface the values in the TYPE column, and the appli‐
cable exemption option is added in parentheses to the end of
the NAME column. (Some device number information might be
made available via the ++||--mm _m option.)
++||--EE ++EE specifies that Linux pipe and Linux UNIX socket files
should be displayed with endpoint information and the files of
the endpoints should also be displayed. Note: UNIX socket
file endpoint information is available only when the compile
flags line of --vv output contains HASUXSOCKEPT.
Pipe endpoint information is displayed in the NAME column in
the form ``_P_I_D_,_c_m_d_,_F_D_m_o_d_e'', where _P_I_D is the endpoint process
ID; _c_m_d is the endpoint process command; _F_D is the endpoint
file's descriptor; and _m_o_d_e is the endpoint file's access
mode.
UNIX socket file endpoint information is displayed in the NAME
column in the form
``type=_T_Y_P_E ->INO=_I_N_O_D_E _P_I_D_,_c_m_d_,_F_D_m_o_d_e'', where _T_Y_P_E is the
socket type; _I_N_O_D_E is the i-node number of the connected
socket; and _P_I_D_, _c_m_d_, _F_D_, and _m_o_d_e are the same as with pipe
endpoint information. Note: UNIX socket file endpoint infor‐
mation is available only when the compile flags line of --vv
output contains HASUXSOCKEPT.
Multiple occurrences of this information can appear in a
file's NAME column.
--EE specfies that Linux pipe and Linux UNIX socket files should
be displayed with endpoint information, but not the files of
the endpoints.
++||--ff [[ccffggGGnn]]
ff by itself clarifies how path name arguments are to be inter‐
preted. When followed by cc, ff, gg, GG, or nn in any combination
it specifies that the listing of kernel file structure infor‐
mation is to be enabled (`+') or inhibited (`-').
Normally a path name argument is taken to be a file system
name if it matches a mounted-on directory name reported by
_m_o_u_n_t(8), or if it represents a block device, named in the
_m_o_u_n_t output and associated with a mounted directory name.
When ++ff is specified, all path name arguments will be taken to
be file system names, and _l_s_o_f will complain if any are not.
This can be useful, for example, when the file system name
(mounted-on device) isn't a block device. This happens for
some CD-ROM file systems.
When --ff is specified by itself, all path name arguments will
be taken to be simple files. Thus, for example, the ``--ff --
/'' arguments direct lsof to search for open files with a `/'
path name, not all open files in the `/' (root) file system.
Be careful to make sure ++ff and --ff are properly terminated and
aren't followed by a character (e.g., of the file or file sys‐
tem name) that might be taken as a parameter. For example,
use ``--'' after ++ff and --ff as in these examples.
$ lsof +f -- /file/system/name
$ lsof -f -- /file/name
The listing of information from kernel file structures,
requested with the ++ff [[ccffggGGnn]] option form, is normally inhib‐
ited, and is not available in whole or part for some dialects
- e.g., /proc-based Linux kernels below 2.6.22. When the pre‐
fix to ff is a plus sign (`+'), these characters request file
structure information:
cc file structure use count (not Linux)
ff file structure address (not Linux)
gg file flag abbreviations (Linux 2.6.22 and up)
GG file flags in hexadecimal (Linux 2.6.22 and up)
nn file structure node address (not Linux)
When the prefix is minus (`-') the same characters disable the
listing of the indicated values.
File structure addresses, use counts, flags, and node
addresses may be used to detect more readily identical files
inherited by child processes and identical files in use by
different processes. _L_s_o_f column output can be sorted by out‐
put columns holding the values and listed to identify identi‐
cal file use, or _l_s_o_f field output can be parsed by an AWK or
Perl post-filter script, or by a C program.
--FF _f specifies a character list, _f, that selects the fields to be
output for processing by another program, and the character
that terminates each output field. Each field to be output is
specified with a single character in _f. The field terminator
defaults to NL, but may be changed to NUL (000). See the OOUUTT‐‐
PPUUTT FFOORR OOTTHHEERR PPRROOGGRRAAMMSS section for a description of the field
identification characters and the field output process.
When the field selection character list is empty, all standard
fields are selected (except the raw device field, security
context and zone field for compatibility reasons) and the NL
field terminator is used.
When the field selection character list contains only a zero
(`0'), all fields are selected (except the raw device field
for compatibility reasons) and the NUL terminator character is
used.
Other combinations of fields and their associated field termi‐
nator character must be set with explicit entries in _f, as
described in the OOUUTTPPUUTT FFOORR OOTTHHEERR PPRROOGGRRAAMMSS section.
When a field selection character identifies an item _l_s_o_f does
not normally list - e.g., PPID, selected with --RR - specifica‐
tion of the field character - e.g., ``--FFRR'' - also selects the
listing of the item.
When the field selection character list contains the single
character `?', _l_s_o_f will display a help list of the field
identification characters. (Escape the `?' character as your
shell requires.)
--gg _[_s_] excludes or selects the listing of files for the processes
whose optional process group IDentification (PGID) numbers are
in the comma-separated set _s - e.g., ``123'' or ``123,^456''.
(There should be no spaces in the set.)
PGID numbers that begin with `^' (negation) represent exclu‐
sions.
Multiple PGID numbers are joined in a single ORed set before
participating in AND option selection. However, PGID exclu‐
sions are applied without ORing or ANDing and take effect
before other selection criteria are applied.
The --gg option also enables the output display of PGID numbers.
When specified without a PGID set that's all it does.
--ii _[_i_] selects the listing of files any of whose Internet address
matches the address specified in _i. If no address is speci‐
fied, this option selects the listing of all Internet and x.25
(HP-UX) network files.
If --ii_4 or --ii_6 is specified with no following address, only
files of the indicated IP version, IPv4 or IPv6, are dis‐
played. (An IPv6 specification may be used only if the
dialects supports IPv6, as indicated by ``[46]'' and
``IPv[46]'' in _l_s_o_f_'_s --hh or --?? output.) Sequentially speci‐
fying --ii4, followed by --ii6 is the same as specifying --ii, and
vice-versa. Specifying --ii4, or --ii6 after --ii is the same as
specifying --ii4 or --ii6 by itself.
Multiple addresses (up to a limit of 100) may be specified
with multiple --ii options. (A port number or service name
range is counted as one address.) They are joined in a single
ORed set before participating in AND option selection.
An Internet address is specified in the form (Items in square
brackets are optional.):
[_4_6][_p_r_o_t_o_c_o_l][@_h_o_s_t_n_a_m_e|_h_o_s_t_a_d_d_r][:_s_e_r_v_i_c_e|_p_o_r_t]
where:
_4_6 specifies the IP version, IPv4 or IPv6
that applies to the following address.
'6' may be be specified only if the UNIX
dialect supports IPv6. If neither '4' nor
'6' is specified, the following address
applies to all IP versions.
_p_r_o_t_o_c_o_l is a protocol name - TTCCPP, UUDDPP
_h_o_s_t_n_a_m_e is an Internet host name. Unless a
specific IP version is specified, open
network files associated with host names
of all versions will be selected.
_h_o_s_t_a_d_d_r is a numeric Internet IPv4 address in
dot form; or an IPv6 numeric address in
colon form, enclosed in brackets, if the
UNIX dialect supports IPv6. When an IP
version is selected, only its numeric
addresses may be specified.
_s_e_r_v_i_c_e is an _/_e_t_c_/_s_e_r_v_i_c_e_s name - e.g., ssmmttpp -
or a list of them.
_p_o_r_t is a port number, or a list of them.
IPv6 options may be used only if the UNIX dialect supports
IPv6. To see if the dialect supports IPv6, run _l_s_o_f and spec‐
ify the --hh or --?? (help) option. If the displayed description
of the --ii option contains ``[46]'' and ``IPv[46]'', IPv6 is
supported.
IPv4 host names and addresses may not be specified if network
file selection is limited to IPv6 with --ii 6. IPv6 host names
and addresses may not be specified if network file selection
is limited to IPv4 with --ii 4. When an open IPv4 network
file's address is mapped in an IPv6 address, the open file's
type will be IPv6, not IPv4, and its display will be selected
by '6', not '4'.
At least one address component - 44,, 66,, _p_r_o_t_o_c_o_l, _h_o_s_t_n_a_m_e,
_h_o_s_t_a_d_d_r, or _s_e_r_v_i_c_e - must be supplied. The `@' character,
leading the host specification, is always required; as is the
`:', leading the port specification. Specify either _h_o_s_t_n_a_m_e
or _h_o_s_t_a_d_d_r. Specify either _s_e_r_v_i_c_e name list or _p_o_r_t number
list. If a _s_e_r_v_i_c_e name list is specified, the _p_r_o_t_o_c_o_l may
also need to be specified if the TCP, UDP and UDPLITE port
numbers for the service name are different. Use any case -
lower or upper - for _p_r_o_t_o_c_o_l.
_S_e_r_v_i_c_e names and _p_o_r_t numbers may be combined in a list whose
entries are separated by commas and whose numeric range
entries are separated by minus signs. There may be no embed‐
ded spaces, and all service names must belong to the specified
_p_r_o_t_o_c_o_l. Since service names may contain embedded minus
signs, the starting entry of a range can't be a service name;
it can be a port number, however.
Here are some sample addresses:
-i6 - IPv6 only
TCP:25 - TCP and port 25
@1.2.3.4 - Internet IPv4 host address 1.2.3.4
@[3ffe:1ebc::1]:1234 - Internet IPv6 host address
3ffe:1ebc::1, port 1234
UDP:who - UDP who service port
TCP@lsof.itap:513 - TCP, port 513 and host name lsof.itap
tcp@foo:1-10,smtp,99 - TCP, ports 1 through 10,
service name _s_m_t_p, port 99, host name foo
tcp@bar:1-smtp - TCP, ports 1 through _s_m_t_p, host bar
:time - either TCP, UDP or UDPLITE time service port
--KK selects the listing of tasks (threads) of processes, on
dialects where task (thread) reporting is supported. (If help
output - i.e., the output of the --hh or --?? options - shows
this option, then task (thread) reporting is supported by the
dialect.)
When --KK and --aa are both specified on Linux, and the tasks of a
main process are selected by other options, the main process
will also be listed as though it were a task, but without a
task ID. (See the description of the TID column in the OOUUTTPPUUTT
section.)
Where the FreeBSD version supports threads, all threads will
be listed with their IDs.
In general threads and tasks inherit the files of the caller,
but may close some and open others, so _l_s_o_f always reports all
the open files of threads and tasks.
--kk _k specifies a kernel name list file, _k, in place of /vmunix,
/mach, etc. --kk is not available under AIX on the IBM
RISC/System 6000.
--ll inhibits the conversion of user ID numbers to login names. It
is also useful when login name lookup is working improperly or
slowly.
++||--LL _[_l_] enables (`+') or disables (`-') the listing of file link
counts, where they are available - e.g., they aren't available
for sockets, or most FIFOs and pipes.
When ++LL is specified without a following number, all link
counts will be listed. When --LL is specified (the default), no
link counts will be listed.
When ++LL is followed by a number, only files having a link
count less than that number will be listed. (No number may
follow --LL.) A specification of the form ``++LL11'' will select
open files that have been unlinked. A specification of the
form ``++aaLL11 _<_f_i_l_e___s_y_s_t_e_m_>'' will select unlinked open files on
the specified file system.
For other link count comparisons, use field output (--FF) and a
post-processing script or program.
++||--mm _m specifies an alternate kernel memory file or activates mount
table supplement processing.
The option form --mm _m specifies a kernel memory file, _m, in
place of _/_d_e_v_/_k_m_e_m or _/_d_e_v_/_m_e_m - e.g., a crash dump file.
The option form ++mm requests that a mount supplement file be
written to the standard output file. All other options are
silently ignored.
There will be a line in the mount supplement file for each
mounted file system, containing the mounted file system direc‐
tory, followed by a single space, followed by the device num‐
ber in hexadecimal "0x" format - e.g.,
/ 0x801
_L_s_o_f can use the mount supplement file to get device numbers
for file systems when it can't get them via _s_t_a_t(2) or
_l_s_t_a_t(2).
The option form ++mm _m identifies _m as a mount supplement file.
Note: the ++mm and ++mm _m options are not available for all sup‐
ported dialects. Check the output of _l_s_o_f_'_s --hh or --?? options
to see if the ++mm and ++mm _m options are available.
++||--MM Enables (++) or disables (--) the reporting of portmapper regis‐
trations for local TCP, UDP and UDPLITE ports, where port map‐
ping is supported. (See the last paragraph of this option
description for information about where portmapper registra‐
tion reporting is supported.)
The default reporting mode is set by the _l_s_o_f builder with the
HASPMAPENABLED #define in the dialect's machine.h header file;
_l_s_o_f is distributed with the HASPMAPENABLED #define deacti‐
vated, so portmapper reporting is disabled by default and must
be requested with ++MM. Specifying _l_s_o_f_'_s --hh or --?? option will
report the default mode. Disabling portmapper registration
when it is already disabled or enabling it when already
enabled is acceptable. When portmapper registration reporting
is enabled, _l_s_o_f displays the portmapper registration (if any)
for local TCP, UDP or UDPLITE ports in square brackets immedi‐
ately following the port numbers or service names - e.g.,
``:1234[name]'' or ``:name[100083]''. The registration infor‐
mation may be a name or number, depending on what the regis‐
tering program supplied to the portmapper when it registered
the port.
When portmapper registration reporting is enabled, _l_s_o_f may
run a little more slowly or even become blocked when access to
the portmapper becomes congested or stopped. Reverse the
reporting mode to determine if portmapper registration report‐
ing is slowing or blocking _l_s_o_f.
For purposes of portmapper registration reporting _l_s_o_f consid‐
ers a TCP, UDP or UDPLITE port local if: it is found in the
local part of its containing kernel structure; or if it is
located in the foreign part of its containing kernel structure
and the local and foreign Internet addresses are the same; or
if it is located in the foreign part of its containing kernel
structure and the foreign Internet address is INADDR_LOOPBACK
(127.0.0.1). This rule may make _l_s_o_f ignore some foreign
ports on machines with multiple interfaces when the foreign
Internet address is on a different interface from the local
one.
See the _l_s_o_f FAQ (The FFAAQQ section gives its location.) for
further discussion of portmapper registration reporting
issues.
Portmapper registration reporting is supported only on
dialects that have RPC header files. (Some Linux distribu‐
tions with GlibC 2.14 do not have them.) When portmapper reg‐
istration reporting is supported, the --hh or --?? help output
will show the ++||--MM option.
--nn inhibits the conversion of network numbers to host names for
network files. Inhibiting conversion may make _l_s_o_f run
faster. It is also useful when host name lookup is not work‐
ing properly.
--NN selects the listing of NFS files.
--oo directs _l_s_o_f to display file offset at all times. It causes
the SIZE/OFF output column title to be changed to OFFSET.
Note: on some UNIX dialects _l_s_o_f can't obtain accurate or con‐
sistent file offset information from its kernel data sources,
sometimes just for particular kinds of files (e.g., socket
files.) Consult the _l_s_o_f FAQ (The FFAAQQ section gives its loca‐
tion.) for more information.
The --oo and --ss options are mutually exclusive; they can't both
be specified. When neither is specified, _l_s_o_f displays what‐
ever value - size or offset - is appropriate and available for
the type of the file.
--oo _o defines the number of decimal digits (_o) to be printed after
the ``0t'' for a file offset before the form is switched to
``0x...''. An _o value of zero (unlimited) directs _l_s_o_f to use
the ``0t'' form for all offset output.
This option does NOT direct _l_s_o_f to display offset at all
times; specify --oo (without a trailing number) to do that. --oo
_o only specifies the number of digits after ``0t'' in either
mixed size and offset or offset-only output. Thus, for exam‐
ple, to direct _l_s_o_f to display offset at all times with a dec‐
imal digit count of 10, use:
-o -o 10
or
-oo10
The default number of digits allowed after ``0t'' is normally
8, but may have been changed by the lsof builder. Consult the
description of the --oo _o option in the output of the --hh or --??
option to determine the default that is in effect.
--OO directs _l_s_o_f to bypass the strategy it uses to avoid being
blocked by some kernel operations - i.e., doing them in forked
child processes. See the BBLLOOCCKKSS AANNDD TTIIMMEEOOUUTTSS and AAVVOOIIDDIINNGG
KKEERRNNEELL BBLLOOCCKKSS sections for more information on kernel opera‐
tions that may block _l_s_o_f.
While use of this option will reduce _l_s_o_f startup overhead, it
may also cause _l_s_o_f to hang when the kernel doesn't respond to
a function. Use this option cautiously.
--pp _s excludes or selects the listing of files for the processes
whose optional process IDentification (PID) numbers are in the
comma-separated set _s - e.g., ``123'' or ``123,^456''. (There
should be no spaces in the set.)
PID numbers that begin with `^' (negation) represent exclu‐
sions.
Multiple process ID numbers are joined in a single ORed set
before participating in AND option selection. However, PID
exclusions are applied without ORing or ANDing and take effect
before other selection criteria are applied.
--PP inhibits the conversion of port numbers to port names for net‐
work files. Inhibiting the conversion may make _l_s_o_f run a
little faster. It is also useful when port name lookup is not
working properly.
++||--rr _[_t_[_m_<_f_m_t_>_]_]
puts _l_s_o_f in repeat mode. There _l_s_o_f lists open files as
selected by other options, delays _t seconds (default fifteen),
then repeats the listing, delaying and listing repetitively
until stopped by a condition defined by the prefix to the
option.
If the prefix is a `-', repeat mode is endless. _L_s_o_f must be
terminated with an interrupt or quit signal.
If the prefix is `+', repeat mode will end the first cycle no
open files are listed - and of course when _l_s_o_f is stopped
with an interrupt or quit signal. When repeat mode ends
because no files are listed, the process exit code will be
zero if any open files were ever listed; one, if none were
ever listed.
_L_s_o_f marks the end of each listing: if field output is in
progress (the --FF, option has been specified), the default
marker is `m'; otherwise the default marker is ``========''.
The marker is followed by a NL character.
The optional "m<fmt>" argument specifies a format for the
marker line. The <fmt> characters following `m' are inter‐
preted as a format specification to the _s_t_r_f_t_i_m_e(3) function,
when both it and the _l_o_c_a_l_t_i_m_e(3) function are available in
the dialect's C library. Consult the _s_t_r_f_t_i_m_e(3) documenta‐
tion for what may appear in its format specification. Note
that when field output is requested with the --FF option, <fmt>
cannot contain the NL format, ``%n''. Note also that when
<fmt> contains spaces or other characters that affect the
shell's interpretation of arguments, <fmt> must be quoted
appropriately.
Repeat mode reduces _l_s_o_f startup overhead, so it is more effi‐
cient to use this mode than to call _l_s_o_f repetitively from a
shell script, for example.
To use repeat mode most efficiently, accompany ++||--rr with spec‐
ification of other _l_s_o_f selection options, so the amount of
kernel memory access _l_s_o_f does will be kept to a minimum.
Options that filter at the process level - e.g., --cc, --gg, --pp,
--uu - are the most efficient selectors.
Repeat mode is useful when coupled with field output (see the
--FF, option description) and a supervising _a_w_k or _P_e_r_l script,
or a C program.
--RR directs lsof to list the Parent Process IDentification number
in the PPID column.
--ss _[_p_:_s_] ss alone directs _l_s_o_f to display file size at all times. It
causes the SIZE/OFF output column title to be changed to SIZE.
If the file does not have a size, nothing is displayed.
The optional --ss _p_:_s form is available only for selected
dialects, and only when the --hh or --?? help output lists it.
When the optional form is available, the ss may be followed by
a protocol name (_p), either TCP or UDP, a colon (`:') and a
comma-separated protocol state name list, the option causes
open TCP and UDP files to be excluded if their state name(s)
are in the list (_s) preceded by a `^'; or included if their
name(s) are not preceded by a `^'.
When an inclusion list is defined, only network files with
state names in the list will be present in the _l_s_o_f output.
Thus, specifying one state name means that only network files
with that lone state name will be listed.
Case is unimportant in the protocol or state names, but there
may be no spaces and the colon (`:') separating the protocol
name (_p) and the state name list (_s) is required.
If only TCP and UDP files are to be listed, as controlled by
the specified exclusions and inclusions, the --ii option must be
specified, too. If only a single protocol's files are to be
listed, add its name as an argument to the --ii option.
For example, to list only network files with TCP state LISTEN,
use:
-iTCP -sTCP:LISTEN
Or, for example, to list network files with all UDP states
except Idle, use:
-iUDP -sUDP:Idle
State names vary with UNIX dialects, so it's not possible to
provide a complete list. Some common TCP state names are:
CLOSED, IDLE, BOUND, LISTEN, ESTABLISHED, SYN_SENT, SYN_RCDV,
ESTABLISHED, CLOSE_WAIT, FIN_WAIT1, CLOSING, LAST_ACK,
FIN_WAIT_2, and TIME_WAIT. Two common UDP state names are
Unbound and Idle.
See the _l_s_o_f FAQ (The FFAAQQ section gives its location.) for
more information on how to use protocol state exclusion and
inclusion, including examples.
The --oo (without a following decimal digit count) and --ss option
(without a following protocol and state name list) are mutu‐
ally exclusive; they can't both be specified. When neither is
specified, _l_s_o_f displays whatever value - size or offset - is
appropriate and available for the type of file.
Since some types of files don't have true sizes - sockets,
FIFOs, pipes, etc. - lsof displays for their sizes the content
amounts in their associated kernel buffers, if possible.
--SS _[_t_] specifies an optional time-out seconds value for kernel func‐
tions - _l_s_t_a_t(2), _r_e_a_d_l_i_n_k(2), and _s_t_a_t(2) - that might other‐
wise deadlock. The minimum for _t is two; the default, fif‐
teen; when no value is specified, the default is used.
See the BBLLOOCCKKSS AANNDD TTIIMMEEOOUUTTSS section for more information.
--TT _[_t_] controls the reporting of some TCP/TPI information, also
reported by _n_e_t_s_t_a_t(1), following the network addresses. In
normal output the information appears in parentheses, each
item except TCP or TPI state name identified by a keyword,
followed by `=', separated from others by a single space:
<TCP or TPI state name>
QR=<read queue length>
QS=<send queue length>
SO=<socket options and values>
SS=<socket states>
TF=<TCP flags and values>
WR=<window read length>
WW=<window write length>
Not all values are reported for all UNIX dialects. Items val‐
ues (when available) are reported after the item name and '='.
When the field output mode is in effect (See OOUUTTPPUUTT FFOORR OOTTHHEERR
PPRROOGGRRAAMMSS.) each item appears as a field with a `T' leading
character.
--TT with no following key characters disables TCP/TPI informa‐
tion reporting.
--TT with following characters selects the reporting of specific
TCP/TPI information:
ff selects reporting of socket options,
states and values, and TCP flags and
values.
qq selects queue length reporting.
ss selects connection state reporting.
ww selects window size reporting.
Not all selections are enabled for some UNIX dialects. State
may be selected for all dialects and is reported by default.
The --hh or --?? help output for the --TT option will show what
selections may be used with the UNIX dialect.
When --TT is used to select information - i.e., it is followed
by one or more selection characters - the displaying of state
is disabled by default, and it must be explicitly selected
again in the characters following --TT. (In effect, then, the
default is equivalent to --TTss.) For example, if queue lengths
and state are desired, use --TTqqss.
Socket options, socket states, some socket values, TCP flags
and one TCP value may be reported (when available in the UNIX
dialect) in the form of the names that commonly appear after
SO_, so_, SS_, TCP_ and TF_ in the dialect's header files -
most often <sys/socket.h>, <sys/socketvar.h> and
<netinet/tcp_var.h>. Consult those header files for the mean‐
ing of the flags, options, states and values.
``SO='' precedes socket options and values; ``SS='', socket
states; and ``TF='', TCP flags and values.
If a flag or option has a value, the value will follow an '='
and the name -- e.g., ``SO=LINGER=5'', ``SO=QLIM=5'',
``TF=MSS=512''. The following seven values may be reported:
Name
Reported Description (Common Symbol)
KEEPALIVE keep alive time (SO_KEEPALIVE)
LINGER linger time (SO_LINGER)
MSS maximum segment size (TCP_MAXSEG)
PQLEN partial listen queue connections
QLEN established listen queue connections
QLIM established listen queue limit
RCVBUF receive buffer length (SO_RCVBUF)
SNDBUF send buffer length (SO_SNDBUF)
Details on what socket options and values, socket states, and
TCP flags and values may be displayed for particular UNIX
dialects may be found in the answer to the ``Why doesn't lsof
report socket options, socket states, and TCP flags and values
for my dialect?'' and ``Why doesn't lsof report the partial
listen queue connection count for my dialect?'' questions in
the _l_s_o_f FAQ (The FFAAQQ section gives its location.)
--tt specifies that _l_s_o_f should produce terse output with process
identifiers only and no header - e.g., so that the output may
be piped to _k_i_l_l(1). --tt selects the --ww option.
--uu _s selects the listing of files for the user whose login names or
user ID numbers are in the comma-separated set _s - e.g.,
``abe'', or ``548,root''. (There should be no spaces in the
set.)
Multiple login names or user ID numbers are joined in a single
ORed set before participating in AND option selection.
If a login name or user ID is preceded by a `^', it becomes a
negation - i.e., files of processes owned by the login name or
user ID will never be listed. A negated login name or user ID
selection is neither ANDed nor ORed with other selections; it
is applied before all other selections and absolutely excludes
the listing of the files of the process. For example, to
direct _l_s_o_f to exclude the listing of files belonging to root
processes, specify ``-u^root'' or ``-u^0''.
--UU selects the listing of UNIX domain socket files.
--vv selects the listing of _l_s_o_f version information, including:
revision number; when the _l_s_o_f binary was constructed; who
constructed the binary and where; the name of the compiler
used to construct the _l_s_o_f _b_i_n_a_r_y_; the version number of the
compiler when readily available; the compiler and loader flags
used to construct the _l_s_o_f binary; and system information,
typically the output of _u_n_a_m_e's --aa option.
--VV directs _l_s_o_f to indicate the items it was asked to list and
failed to find - command names, file names, Internet addresses
or files, login names, NFS files, PIDs, PGIDs, and UIDs.
When other options are ANDed to search options, or com‐
pile-time options restrict the listing of some files, _l_s_o_f may
not report that it failed to find a search item when an ANDed
option or compile-time option prevents the listing of the open
file containing the located search item.
For example, ``lsof -V -iTCP@foobar -a -d 999'' may not report
a failure to locate open files at ``TCP@foobar'' and may not
list any, if none have a file descriptor number of 999. A
similar situation arises when HASSECURITY and HASNOSOCKSECU‐
RITY are defined at compile time and they prevent the listing
of open files.
++||--ww Enables (++) or disables (--) the suppression of warning mes‐
sages.
The _l_s_o_f builder may choose to have warning messages disabled
or enabled by default. The default warning message state is
indicated in the output of the --hh or --?? option. Disabling
warning messages when they are already disabled or enabling
them when already enabled is acceptable.
The --tt option selects the --ww option.
--xx _[_f_l_] may accompany the ++dd and ++DD options to direct their processing
to cross over symbolic links and|or file system mount points
encountered when scanning the directory (++dd) or directory tree
(++DD).
If --xx is specified by itself without a following parameter,
cross-over processing of both symbolic links and file system
mount points is enabled. Note that when --xx is specified with‐
out a parameter, the next argument must begin with '-' or '+'.
The optional 'f' parameter enables file system mount point
cross-over processing; 'l', symbolic link cross-over process‐
ing.
The --xx option may not be supplied without also supplying a ++dd
or ++DD option.
--XX This is a dialect-specific option.
AIX:
This IBM AIX RISC/System 6000 option requests the reporting of
executed text file and shared library references.
WWAARRNNIINNGG:: because this option uses the kernel readx() function,
its use on a busy AIX system might cause an application
process to hang so completely that it can neither be killed
nor stopped. I have never seen this happen or had a report of
its happening, but I think there is a remote possibility it
could happen.
By default use of readx() is disabled. On AIX 5L and above
_l_s_o_f may need setuid-root permission to perform the actions
this option requests.
The _l_s_o_f builder may specify that the --XX option be restricted
to processes whose real UID is root. If that has been done,
the --XX option will not appear in the --hh or --?? help output
unless the real UID of the _l_s_o_f process is root. The default
_l_s_o_f distribution allows any UID to specify --XX,, so by default
it will appear in the help output.
When AIX readx() use is disabled, _l_s_o_f may not be able to
report information for all text and loader file references,
but it may also avoid exacerbating an AIX kernel directory
search kernel error, known as the Stale Segment ID bug.
The readx() function, used by _l_s_o_f or any other program to
access some sections of kernel virtual memory, can trigger the
Stale Segment ID bug. It can cause the kernel's dir_search()
function to believe erroneously that part of an in-memory copy
of a file system directory has been zeroed. Another applica‐
tion process, distinct from _l_s_o_f, asking the kernel to search
the directory - e.g., by using _o_p_e_n(2) - can cause
dir_search() to loop forever, thus hanging the application
process.
Consult the _l_s_o_f FAQ (The FFAAQQ section gives its location.)
and the _0_0_R_E_A_D_M_E file of the _l_s_o_f distribution for a more com‐
plete description of the Stale Segment ID bug, its APAR, and
methods for defining readx() use when compiling _l_s_o_f.
Linux:
This Linux option requests that _l_s_o_f skip the reporting of
information on all open TCP, UDP and UDPLITE IPv4 and IPv6
files.
This Linux option is most useful when the system has an
extremely large number of open TCP, UDP and UDPLITE files, the
processing of whose information in the _/_p_r_o_c_/_n_e_t_/_t_c_p_* and
_/_p_r_o_c_/_n_e_t_/_u_d_p_* files would take _l_s_o_f a long time, and whose
reporting is not of interest.
Use this option with care and only when you are sure that the
information you want _l_s_o_f to display isn't associated with
open TCP, UDP or UDPLITE socket files.
Solaris 10 and above:
This Solaris 10 and above option requests the reporting of
cached paths for files that have been deleted - i.e., removed
with _r_m(1) or _u_n_l_i_n_k(2).
The cached path is followed by the string `` (deleted)'' to
indicate that the path by which the file was opened has been
deleted.
Because intervening changes made to the path - i.e., renames
with _m_v(1) or _r_e_n_a_m_e(2) - are not recorded in the cached path,
what _l_s_o_f reports is only the path by which the file was
opened, not its possibly different final path.
--zz _[_z_] specifies how Solaris 10 and higher zone information is to be
handled.
Without a following argument - e.g., NO _z - the option speci‐
fies that zone names are to be listed in the ZONE output col‐
umn.
The --zz option may be followed by a zone name, zz_. That causes
lsof to list only open files for processes in that zone. Mul‐
tiple --zz _z option and argument pairs may be specified to form
a list of named zones. Any open file of any process in any of
the zones will be listed, subject to other conditions speci‐
fied by other options and arguments.
--ZZ _[_Z_] specifies how SELinux security contexts are to be handled. It
and 'Z' field output character support are inhibited when
SELinux is disabled in the running Linux kernel. See OOUUTTPPUUTT
FFOORR OOTTHHEERR PPRROOGGRRAAMMSS for more information on the 'Z' field out‐
put character.
Without a following argument - e.g., NO _Z - the option speci‐
fies that security contexts are to be listed in the SECU‐
RITY-CONTEXT output column.
The --ZZ option may be followed by a wildcard security context
name, ZZ_. That causes lsof to list only open files for pro‐
cesses in that security context. Multiple --ZZ _Z option and
argument pairs may be specified to form a list of security
contexts. Any open file of any process in any of the security
contexts will be listed, subject to other conditions specified
by other options and arguments. Note that _Z can be A:B:C or
*:B:C or A:B:* or *:*:C to match against the A:B:C context.
---- The double minus sign option is a marker that signals the end
of the keyed options. It may be used, for example, when the
first file name begins with a minus sign. It may also be used
when the absence of a value for the last keyed option must be
signified by the presence of a minus sign in the following
option and before the start of the file names.
_n_a_m_e_s These are path names of specific files to list. Symbolic
links are resolved before use. The first name may be sepa‐
rated from the preceding options with the ``--'' option.
If a _n_a_m_e is the mounted-on directory of a file system or the
device of the file system, _l_s_o_f will list all the files open
on the file system. To be considered a file system, the _n_a_m_e
must match a mounted-on directory name in _m_o_u_n_t(8) output, or
match the name of a block device associated with a mounted-on
directory name. The ++||--ff option may be used to force _l_s_o_f to
consider a _n_a_m_e a file system identifier (++ff) or a simple file
(--ff).
If _n_a_m_e is a path to a directory that is not the mounted-on
directory name of a file system, it is treated just as a regu‐
lar file is treated - i.e., its listing is restricted to pro‐
cesses that have it open as a file or as a process-specific
directory, such as the root or current working directory. To
request that _l_s_o_f look for open files inside a directory name,
use the ++dd _s and ++DD _D options.
If a _n_a_m_e is the base name of a family of multiplexed files -
e.g, AIX's _/_d_e_v_/_p_t_[_c_s_] - _l_s_o_f will list all the associated
multiplexed files on the device that are open - e.g.,
_/_d_e_v_/_p_t_[_c_s_]_/_1, _/_d_e_v_/_p_t_[_c_s_]_/_2, etc.
If a _n_a_m_e is a UNIX domain socket name, _l_s_o_f will usually
search for it by the characters of the name alone - exactly as
it is specified and is recorded in the kernel socket struc‐
ture. (See the next paragraph for an exception to that rule
for Linux.) Specifying a relative path - e.g., _._/_f_i_l_e - in
place of the file's absolute path - e.g., _/_t_m_p_/_f_i_l_e - won't
work because _l_s_o_f must match the characters you specify with
what it finds in the kernel UNIX domain socket structures.
If a _n_a_m_e is a Linux UNIX domain socket name, in one case _l_s_o_f
is able to search for it by its device and inode number,
allowing _n_a_m_e to be a relative path. The case requires that
the absolute path -- i.e., one beginning with a slash ('/') be
used by the process that created the socket, and hence be
stored in the _/_p_r_o_c_/_n_e_t_/_u_n_i_x file; and it requires that _l_s_o_f
be able to obtain the device and node numbers of both the
absolute path in _/_p_r_o_c_/_n_e_t_/_u_n_i_x and _n_a_m_e via successful
_s_t_a_t(2) system calls. When those conditions are met, _l_s_o_f
will be able to search for the UNIX domain socket when some
path to it is is specified in _n_a_m_e. Thus, for example, if the
path is _/_d_e_v_/_l_o_g, and an _l_s_o_f search is initiated when the
working directory is _/_d_e_v, then _n_a_m_e could be _._/_l_o_g.
If a _n_a_m_e is none of the above, _l_s_o_f will list any open files
whose device and inode match that of the specified path _n_a_m_e.
If you have also specified the --bb option, the only _n_a_m_e_s you
may safely specify are file systems for which your mount table
supplies alternate device numbers. See the AAVVOOIIDDIINNGG KKEERRNNEELL
BBLLOOCCKKSS and AALLTTEERRNNAATTEE DDEEVVIICCEE NNUUMMBBEERRSS sections for more informa‐
tion.
Multiple file names are joined in a single ORed set before
participating in AND option selection.
AAFFSS
_L_s_o_f supports the recognition of AFS files for these dialects (and AFS
versions):
AIX 4.1.4 (AFS 3.4a)
HP-UX 9.0.5 (AFS 3.4a)
Linux 1.2.13 (AFS 3.3)
Solaris 2.[56] (AFS 3.4a)
It may recognize AFS files on other versions of these dialects, but has
not been tested there. Depending on how AFS is implemented, _l_s_o_f may
recognize AFS files in other dialects, or may have difficulties recog‐
nizing AFS files in the supported dialects.
_L_s_o_f may have trouble identifying all aspects of AFS files in supported
dialects when AFS kernel support is implemented via dynamic modules
whose addresses do not appear in the kernel's variable name list. In
that case, _l_s_o_f may have to guess at the identity of AFS files, and
might not be able to obtain volume information from the kernel that is
needed for calculating AFS volume node numbers. When _l_s_o_f can't com‐
pute volume node numbers, it reports blank in the NODE column.
The --AA _A option is available in some dialect implementations of _l_s_o_f
for specifying the name list file where dynamic module kernel addresses
may be found. When this option is available, it will be listed in the
_l_s_o_f help output, presented in response to the --hh or --??
See the _l_s_o_f FAQ (The FFAAQQ section gives its location.) for more infor‐
mation about dynamic modules, their symbols, and how they affect _l_s_o_f
options.
Because AFS path lookups don't seem to participate in the kernel's name
cache operations, _l_s_o_f can't identify path name components for AFS
files.
SSEECCUURRIITTYY
_L_s_o_f has three features that may cause security concerns. First, its
default compilation mode allows anyone to list all open files with it.
Second, by default it creates a user-readable and user-writable device
cache file in the home directory of the real user ID that executes
_l_s_o_f. (The list-all-open-files and device cache features may be dis‐
abled when _l_s_o_f is compiled.) Third, its --kk and --mm options name alter‐
nate kernel name list or memory files.
Restricting the listing of all open files is controlled by the com‐
pile-time HASSECURITY and HASNOSOCKSECURITY options. When HASSECURITY
is defined, _l_s_o_f will allow only the root user to list all open files.
The non-root user may list only open files of processes with the same
user IDentification number as the real user ID number of the _l_s_o_f
process (the one that its user logged on with).
However, if HASSECURITY and HASNOSOCKSECURITY are both defined, anyone
may list open socket files, provided they are selected with the --ii
option.
When HASSECURITY is not defined, anyone may list all open files.
Help output, presented in response to the --hh or --?? option, gives the
status of the HASSECURITY and HASNOSOCKSECURITY definitions.
See the SSeeccuurriittyy section of the _0_0_R_E_A_D_M_E file of the _l_s_o_f distribution
for information on building _l_s_o_f with the HASSECURITY and HASNOSOCKSE‐
CURITY options enabled.
Creation and use of a user-readable and user-writable device cache file
is controlled by the compile-time HASDCACHE option. See the DDEEVVIICCEE
CCAACCHHEE FFIILLEE section and the sections that follow it for details on how
its path is formed. For security considerations it is important to
note that in the default _l_s_o_f distribution, if the real user ID under
which _l_s_o_f is executed is root, the device cache file will be written
in root's home directory - e.g., _/ or _/_r_o_o_t. When HASDCACHE is not
defined, _l_s_o_f does not write or attempt to read a device cache file.
When HASDCACHE is defined, the _l_s_o_f help output, presented in response
to the --hh, --DD??, or --?? options, will provide device cache file handling
information. When HASDCACHE is not defined, the --hh or --?? output will
have no --DD option description.
Before you decide to disable the device cache file feature - enabling
it improves the performance of _l_s_o_f by reducing the startup overhead of
examining all the nodes in _/_d_e_v (or _/_d_e_v_i_c_e_s) - read the discussion of
it in the _0_0_D_C_A_C_H_E file of the _l_s_o_f distribution and the _l_s_o_f FAQ (The
FFAAQQ section gives its location.)
WHEN IN DOUBT, YOU CAN TEMPORARILY DISABLE THE USE OF THE DEVICE CACHE
FILE WITH THE --DDii OPTION.
When _l_s_o_f user declares alternate kernel name list or memory files with
the --kk and --mm options, _l_s_o_f checks the user's authority to read them
with _a_c_c_e_s_s(2). This is intended to prevent whatever special power
_l_s_o_f_'_s modes might confer on it from letting it read files not normally
accessible via the authority of the real user ID.
OOUUTTPPUUTT
This section describes the information _l_s_o_f lists for each open file.
See the OOUUTTPPUUTT FFOORR OOTTHHEERR PPRROOGGRRAAMMSS section for additional information on
output that can be processed by another program.
_L_s_o_f only outputs printable (declared so by _i_s_p_r_i_n_t(3)) 8 bit charac‐
ters. Non-printable characters are printed in one of three forms: the
C ``\[bfrnt]'' form; the control character `^' form (e.g., ``^@''); or
hexadecimal leading ``\x'' form (e.g., ``\xab''). Space is non-print‐
able in the COMMAND column (``\x20'') and printable elsewhere.
For some dialects - if HASSETLOCALE is defined in the dialect's
machine.h header file - _l_s_o_f will print the extended 8 bit characters
of a language locale. The _l_s_o_f process must be supplied a language
locale environment variable (e.g., LANG) whose value represents a known
language locale in which the extended characters are considered print‐
able by _i_s_p_r_i_n_t(3). Otherwise _l_s_o_f considers the extended characters
non-printable and prints them according to its rules for non-printable
characters, stated above. Consult your dialect's _s_e_t_l_o_c_a_l_e(3) man page
for the names of other environment variables that may be used in place
of LANG - e.g., LC_ALL, LC_CTYPE, etc.
_L_s_o_f_'_s language locale support for a dialect also covers wide charac‐
ters - e.g., UTF-8 - when HASSETLOCALE and HASWIDECHAR are defined in
the dialect's machine.h header file, and when a suitable language
locale has been defined in the appropriate environment variable for the
_l_s_o_f process. Wide characters are printable under those conditions if
_i_s_w_p_r_i_n_t(3) reports them to be. If HASSETLOCALE, HASWIDECHAR and a
suitable language locale aren't defined, or if _i_s_w_p_r_i_n_t(3) reports wide
characters that aren't printable, _l_s_o_f considers the wide characters
non-printable and prints each of their 8 bits according to its rules
for non-printable characters, stated above.
Consult the answers to the "Language locale support" questions in the
lsof FAQ (The FFAAQQ section gives its location.) for more information.
_L_s_o_f dynamically sizes the output columns each time it runs, guarantee‐
ing that each column is a minimum size. It also guarantees that each
column is separated from its predecessor by at least one space.
COMMAND contains the first nine characters of the name of the UNIX
command associated with the process. If a non-zero _w value
is specified to the ++cc _w option, the column contains the
first _w characters of the name of the UNIX command associ‐
ated with the process up to the limit of characters supplied
to _l_s_o_f by the UNIX dialect. (See the description of the ++cc
_w command or the _l_s_o_f FAQ for more information. The FFAAQQ
section gives its location.)
If _w is less than the length of the column title, ``COM‐
MAND'', it will be raised to that length.
If a zero _w value is specified to the ++cc _w option, the col‐
umn contains all the characters of the name of the UNIX com‐
mand associated with the process.
All command name characters maintained by the kernel in its
structures are displayed in field output when the command
name descriptor (`c') is specified. See the OOUUTTPPUUTT FFOORR
OOTTHHEERR CCOOMMMMAANNDDSS section for information on selecting field
output and the associated command name descriptor.
PID is the Process IDentification number of the process.
TID is the task (thread) IDentification number, if task (thread)
reporting is supported by the dialect and a task (thread) is
being listed. (If help output - i.e., the output of the --hh
or --?? options - shows this option, then task (thread)
reporting is supported by the dialect.)
A blank TID column in Linux indicates a process - i.e., a
non-task.
ZONE is the Solaris 10 and higher zone name. This column must be
selected with the --zz option.
SECURITY-CONTEXT
is the SELinux security context. This column must be
selected with the --ZZ option. Note that the --ZZ option is
inhibited when SELinux is disabled in the running Linux ker‐
nel.
PPID is the Parent Process IDentification number of the process.
It is only displayed when the --RR option has been specified.
PGID is the process group IDentification number associated with
the process. It is only displayed when the --gg option has
been specified.
USER is the user ID number or login name of the user to whom the
process belongs, usually the same as reported by _p_s(1).
However, on Linux USER is the user ID number or login that
owns the directory in /proc where _l_s_o_f finds information
about the process. Usually that is the same value reported
by _p_s(1), but may differ when the process has changed its
effective user ID. (See the --ll option description for
information on when a user ID number or login name is dis‐
played.)
FD is the File Descriptor number of the file or:
ccwwdd current working directory;
LL_n_n library references (AIX);
eerrrr FD information error (see NAME column);
jjlldd jail directory (FreeBSD);
llttxx shared library text (code and data);
MMxxxx hex memory-mapped type number xx.
mm8866 DOS Merge mapped file;
mmeemm memory-mapped file;
mmmmaapp memory-mapped device;
ppdd parent directory;
rrttdd root directory;
ttrr kernel trace file (OpenBSD);
ttxxtt program text (code and data);
vv8866 VP/ix mapped file;
FD is followed by one of these characters, describing the
mode under which the file is open:
rr for read access;
ww for write access;
uu for read and write access;
space if mode unknown and no lock
character follows;
`-' if mode unknown and lock
character follows.
The mode character is followed by one of these lock charac‐
ters, describing the type of lock applied to the file:
NN for a Solaris NFS lock of unknown type;
rr for read lock on part of the file;
RR for a read lock on the entire file;
ww for a write lock on part of the file;
WW for a write lock on the entire file;
uu for a read and write lock of any length;
UU for a lock of unknown type;
xx for an SCO OpenServer Xenix lock on part of the
file;
XX for an SCO OpenServer Xenix lock on the entire file;
space if there is no lock.
See the LLOOCCKKSS section for more information on the lock
information character.
The FD column contents constitutes a single field for pars‐
ing in post-processing scripts.
TYPE is the type of the node associated with the file - e.g.,
GDIR, GREG, VDIR, VREG, etc.
or ``IPv4'' for an IPv4 socket;
or ``IPv6'' for an open IPv6 network file - even if its
address is IPv4, mapped in an IPv6 address;
or ``ax25'' for a Linux AX.25 socket;
or ``inet'' for an Internet domain socket;
or ``lla'' for a HP-UX link level access file;
or ``rte'' for an AF_ROUTE socket;
or ``sock'' for a socket of unknown domain;
or ``unix'' for a UNIX domain socket;
or ``x.25'' for an HP-UX x.25 socket;
or ``BLK'' for a block special file;
or ``CHR'' for a character special file;
or ``DEL'' for a Linux map file that has been deleted;
or ``DIR'' for a directory;
or ``DOOR'' for a VDOOR file;
or ``FIFO'' for a FIFO special file;
or ``KQUEUE'' for a BSD style kernel event queue file;
or ``LINK'' for a symbolic link file;
or ``MPB'' for a multiplexed block file;
or ``MPC'' for a multiplexed character file;
or ``NOFD'' for a Linux /proc/<PID>/fd directory that can't
be opened -- the directory path appears in the NAME column,
followed by an error message;
or ``PAS'' for a _/_p_r_o_c_/_a_s file;
or ``PAXV'' for a _/_p_r_o_c_/_a_u_x_v file;
or ``PCRE'' for a _/_p_r_o_c_/_c_r_e_d file;
or ``PCTL'' for a _/_p_r_o_c control file;
or ``PCUR'' for the current _/_p_r_o_c process;
or ``PCWD'' for a _/_p_r_o_c current working directory;
or ``PDIR'' for a _/_p_r_o_c directory;
or ``PETY'' for a _/_p_r_o_c executable type (_e_t_y_p_e);
or ``PFD'' for a _/_p_r_o_c file descriptor;
or ``PFDR'' for a _/_p_r_o_c file descriptor directory;
or ``PFIL'' for an executable _/_p_r_o_c file;
or ``PFPR'' for a _/_p_r_o_c FP register set;
or ``PGD'' for a _/_p_r_o_c_/_p_a_g_e_d_a_t_a file;
or ``PGID'' for a _/_p_r_o_c group notifier file;
or ``PIPE'' for pipes;
or ``PLC'' for a _/_p_r_o_c_/_l_w_p_c_t_l file;
or ``PLDR'' for a _/_p_r_o_c_/_l_p_w directory;
or ``PLDT'' for a _/_p_r_o_c_/_l_d_t file;
or ``PLPI'' for a _/_p_r_o_c_/_l_p_s_i_n_f_o file;
or ``PLST'' for a _/_p_r_o_c_/_l_s_t_a_t_u_s file;
or ``PLU'' for a _/_p_r_o_c_/_l_u_s_a_g_e file;
or ``PLWG'' for a _/_p_r_o_c_/_g_w_i_n_d_o_w_s file;
or ``PLWI'' for a _/_p_r_o_c_/_l_w_p_s_i_n_f_o file;
or ``PLWS'' for a _/_p_r_o_c_/_l_w_p_s_t_a_t_u_s file;
or ``PLWU'' for a _/_p_r_o_c_/_l_w_p_u_s_a_g_e file;
or ``PLWX'' for a _/_p_r_o_c_/_x_r_e_g_s file;
or ``PMAP'' for a _/_p_r_o_c map file (_m_a_p);
or ``PMEM'' for a _/_p_r_o_c memory image file;
or ``PNTF'' for a _/_p_r_o_c process notifier file;
or ``POBJ'' for a _/_p_r_o_c_/_o_b_j_e_c_t file;
or ``PODR'' for a _/_p_r_o_c_/_o_b_j_e_c_t directory;
or ``POLP'' for an old format _/_p_r_o_c light weight process
file;
or ``POPF'' for an old format _/_p_r_o_c PID file;
or ``POPG'' for an old format _/_p_r_o_c page data file;
or ``PORT'' for a SYSV named pipe;
or ``PREG'' for a _/_p_r_o_c register file;
or ``PRMP'' for a _/_p_r_o_c_/_r_m_a_p file;
or ``PRTD'' for a _/_p_r_o_c root directory;
or ``PSGA'' for a _/_p_r_o_c_/_s_i_g_a_c_t file;
or ``PSIN'' for a _/_p_r_o_c_/_p_s_i_n_f_o file;
or ``PSTA'' for a _/_p_r_o_c status file;
or ``PSXSEM'' for a POSIX semaphore file;
or ``PSXSHM'' for a POSIX shared memory file;
or ``PUSG'' for a _/_p_r_o_c_/_u_s_a_g_e file;
or ``PW'' for a _/_p_r_o_c_/_w_a_t_c_h file;
or ``PXMP'' for a _/_p_r_o_c_/_x_m_a_p file;
or ``REG'' for a regular file;
or ``SMT'' for a shared memory transport file;
or ``STSO'' for a stream socket;
or ``UNNM'' for an unnamed type file;
or ``XNAM'' for an OpenServer Xenix special file of unknown
type;
or ``XSEM'' for an OpenServer Xenix semaphore file;
or ``XSD'' for an OpenServer Xenix shared data file;
or the four type number octets if the corresponding name
isn't known.
FILE-ADDR contains the kernel file structure address when ff has been
specified to ++ff;
FCT contains the file reference count from the kernel file
structure when cc has been specified to ++ff;
FILE-FLAG when gg or GG has been specified to ++ff, this field contains
the contents of the f_flag[s] member of the kernel file
structure and the kernel's per-process open file flags (if
available); `G' causes them to be displayed in hexadecimal;
`g', as short-hand names; two lists may be displayed with
entries separated by commas, the lists separated by a semi‐
colon (`;'); the first list may contain short-hand names for
f_flag[s] values from the following table:
AIO asynchronous I/O (e.g., FAIO)
AP append
ASYN asynchronous I/O (e.g., FASYNC)
BAS block, test, and set in use
BKIU block if in use
BL use block offsets
BSK block seek
CA copy avoid
CIO concurrent I/O
CLON clone
CLRD CL read
CR create
DF defer
DFI defer IND
DFLU data flush
DIR direct
DLY delay
DOCL do clone
DSYN data-only integrity
DTY must be a directory
EVO event only
EX open for exec
EXCL exclusive open
FSYN synchronous writes
GCDF defer during unp_gc() (AIX)
GCMK mark during unp_gc() (AIX)
GTTY accessed via /dev/tty
HUP HUP in progress
KERN kernel
KIOC kernel-issued ioctl
LCK has lock
LG large file
MBLK stream message block
MK mark
MNT mount
MSYN multiplex synchronization
NATM don't update atime
NB non-blocking I/O
NBDR no BDRM check
NBIO SYSV non-blocking I/O
NBF n-buffering in effect
NC no cache
ND no delay
NDSY no data synchronization
NET network
NFLK don't follow links
NMFS NM file system
NOTO disable background stop
NSH no share
NTTY no controlling TTY
OLRM OLR mirror
PAIO POSIX asynchronous I/O
PP POSIX pipe
R read
RC file and record locking cache
REV revoked
RSH shared read
RSYN read synchronization
RW read and write access
SL shared lock
SNAP cooked snapshot
SOCK socket
SQSH Sequent shared set on open
SQSV Sequent SVM set on open
SQR Sequent set repair on open
SQS1 Sequent full shared open
SQS2 Sequent partial shared open
STPI stop I/O
SWR synchronous read
SYN file integrity while writing
TCPM avoid TCP collision
TR truncate
W write
WKUP parallel I/O synchronization
WTG parallel I/O synchronization
VH vhangup pending
VTXT virtual text
XL exclusive lock
this list of names was derived from F* #define's in dialect
header files <fcntl.h>, <linux</fs.h>, <sys/fcntl.c>,
<sys/fcntlcom.h>, and <sys/file.h>; see the lsof.h header
file for a list showing the correspondence between the above
short-hand names and the header file definitions;
the second list (after the semicolon) may contain short-hand
names for kernel per-process open file flags from this ta‐
ble:
ALLC allocated
BR the file has been read
BHUP activity stopped by SIGHUP
BW the file has been written
CLSG closing
CX close-on-exec (see fcntl(F_SETFD))
LCK lock was applied
MP memory-mapped
OPIP open pending - in progress
RSVW reserved wait
SHMT UF_FSHMAT set (AIX)
USE in use (multi-threaded)
NODE-ID (or INODE-ADDR for some dialects) contains a unique identi‐
fier for the file node (usually the kernel vnode or inode
address, but also occasionally a concatenation of device and
node number) when nn has been specified to ++ff;
DEVICE contains the device numbers, separated by commas, for a
character special, block special, regular, directory or NFS
file;
or ``memory'' for a memory file system node under Tru64
UNIX;
or the address of the private data area of a Solaris socket
stream;
or a kernel reference address that identifies the file (The
kernel reference address may be used for FIFO's, for exam‐
ple.);
or the base address or device name of a Linux AX.25 socket
device.
Usually only the lower thirty two bits of Tru64 UNIX kernel
addresses are displayed.
SIZE, SIZE/OFF, or OFFSET
is the size of the file or the file offset in bytes. A
value is displayed in this column only if it is available.
_L_s_o_f displays whatever value - size or offset - is appropri‐
ate for the type of the file and the version of _l_s_o_f.
On some UNIX dialects _l_s_o_f can't obtain accurate or consis‐
tent file offset information from its kernel data sources,
sometimes just for particular kinds of files (e.g., socket
files.) In other cases, files don't have true sizes - e.g.,
sockets, FIFOs, pipes - so _l_s_o_f displays for their sizes the
content amounts it finds in their kernel buffer descriptors
(e.g., socket buffer size counts or TCP/IP window sizes.)
Consult the _l_s_o_f FAQ (The FFAAQQ section gives its location.)
for more information.
The file size is displayed in decimal; the offset is nor‐
mally displayed in decimal with a leading ``0t'' if it con‐
tains 8 digits or less; in hexadecimal with a leading ``0x''
if it is longer than 8 digits. (Consult the --oo _o option
description for information on when 8 might default to some
other value.)
Thus the leading ``0t'' and ``0x'' identify an offset when
the column may contain both a size and an offset (i.e., its
title is SIZE/OFF).
If the --oo option is specified, _l_s_o_f always displays the file
offset (or nothing if no offset is available) and labels the
column OFFSET. The offset always begins with ``0t'' or
``0x'' as described above.
The _l_s_o_f user can control the switch from ``0t'' to ``0x''
with the --oo _o option. Consult its description for more
information.
If the --ss option is specified, _l_s_o_f always displays the file
size (or nothing if no size is available) and labels the
column SIZE. The --oo and --ss options are mutually exclusive;
they can't both be specified.
For files that don't have a fixed size - e.g., don't reside
on a disk device - _l_s_o_f will display appropriate information
about the current size or position of the file if it is
available in the kernel structures that define the file.
NLINK contains the file link count when ++LL has been specified;
NODE is the node number of a local file;
or the inode number of an NFS file in the server host;
or the Internet protocol type - e.g, ``TCP'';
or ``STR'' for a stream;
or ``CCITT'' for an HP-UX x.25 socket;
or the IRQ or inode number of a Linux AX.25 socket device.
NAME is the name of the mount point and file system on which the
file resides;
or the name of a file specified in the _n_a_m_e_s option (after
any symbolic links have been resolved);
or the name of a character special or block special device;
or the local and remote Internet addresses of a network
file; the local host name or IP number is followed by a
colon (':'), the port, ``->'', and the two-part remote
address; IP addresses may be reported as numbers or names,
depending on the ++||--MM, --nn, and --PP options; colon-separated
IPv6 numbers are enclosed in square brackets; IPv4
INADDR_ANY and IPv6 IN6_IS_ADDR_UNSPECIFIED addresses, and
zero port numbers are represented by an asterisk ('*'); a
UDP destination address may be followed by the amount of
time elapsed since the last packet was sent to the destina‐
tion; TCP, UDP and UDPLITE remote addresses may be followed
by TCP/TPI information in parentheses - state (e.g.,
``(ESTABLISHED)'', ``(Unbound)''), queue sizes, and window
sizes (not all dialects) - in a fashion similar to what _n_e_t_‐
_s_t_a_t(1) reports; see the --TT option description or the
description of the TCP/TPI field in OOUUTTPPUUTT FFOORR OOTTHHEERR PPRROO‐‐
GGRRAAMMSS for more information on state, queue size, and window
size;
or the address or name of a UNIX domain socket, possibly
including a stream clone device name, a file system object's
path name, local and foreign kernel addresses, socket pair
information, and a bound vnode address;
or the local and remote mount point names of an NFS file;
or ``STR'', followed by the stream name;
or a stream character device name, followed by ``->'' and
the stream name or a list of stream module names, separated
by ``->'';
or ``STR:'' followed by the SCO OpenServer stream device and
module names, separated by ``->'';
or system directory name, `` -- '', and as many components
of the path name as _l_s_o_f can find in the kernel's name cache
for selected dialects (See the KKEERRNNEELL NNAAMMEE CCAACCHHEE section for
more information.);
or ``PIPE->'', followed by a Solaris kernel pipe destination
address;
or ``COMMON:'', followed by the vnode device information
structure's device name, for a Solaris common vnode;
or the address family, followed by a slash (`/'), followed
by fourteen comma-separated bytes of a non-Internet raw
socket address;
or the HP-UX x.25 local address, followed by the virtual
connection number (if any), followed by the remote address
(if any);
or ``(dead)'' for disassociated Tru64 UNIX files - typically
terminal files that have been flagged with the TIOCNOTTY
ioctl and closed by daemons;
or ``rd=<offset>'' and ``wr=<offset>'' for the values of the
read and write offsets of a FIFO;
or ``clone _n:/dev/event'' for SCO OpenServer file clones of
the _/_d_e_v_/_e_v_e_n_t device, where _n is the minor device number of
the file;
or ``(socketpair: n)'' for a Solaris 2.6, 8, 9 or 10 UNIX
domain socket, created by the _s_o_c_k_e_t_p_a_i_r(3N) network func‐
tion;
or ``no PCB'' for socket files that do not have a protocol
block associated with them, optionally followed by ``,
CANTSENDMORE'' if sending on the socket has been disabled,
or ``, CANTRCVMORE'' if receiving on the socket has been
disabled (e.g., by the _s_h_u_t_d_o_w_n(2) function);
or the local and remote addresses of a Linux IPX socket file
in the form <net>:[<node>:]<port>, followed in parentheses
by the transmit and receive queue sizes, and the connection
state;
or ``dgram'' or ``stream'' for the type UnixWare 7.1.1 and
above in-kernel UNIX domain sockets, followed by a colon
(':') and the local path name when available, followed by
``->'' and the remote path name or kernel socket address in
hexadecimal when available;
or the association value, association index, endpoint value,
local address, local port, remote address and remote port
for Linux SCTP sockets;
or ``protocol: '' followed by the Linux socket's protocol
attribute.
For dialects that support a ``namefs'' file system, allowing one file
to be attached to another with _f_a_t_t_a_c_h(3C), _l_s_o_f will add
``(FA:<address1><direction><address2>)'' to the NAME column.
<address1> and <address2> are hexadecimal vnode addresses. <direction>
will be ``<-'' if <address2> has been fattach'ed to this vnode whose
address is <address1>; and ``->'' if <address1>, the vnode address of
this vnode, has been fattach'ed to <address2>. <address1> may be omit‐
ted if it already appears in the DEVICE column.
_L_s_o_f may add two parenthetical notes to the NAME column for open
Solaris 10 files: ``(?)'' if _l_s_o_f considers the path name of question‐
able accuracy; and ``(deleted)'' if the --XX option has been specified
and _l_s_o_f detects the open file's path name has been deleted. Consult
the _l_s_o_f FAQ (The FFAAQQ section gives its location.) for more informa‐
tion on these NAME column additions.
LLOOCCKKSS
_L_s_o_f can't adequately report the wide variety of UNIX dialect file
locks in a single character. What it reports in a single character is
a compromise between the information it finds in the kernel and the
limitations of the reporting format.
Moreover, when a process holds several byte level locks on a file, _l_s_o_f
only reports the status of the first lock it encounters. If it is a
byte level lock, then the lock character will be reported in lower case
- i.e., `r', `w', or `x' - rather than the upper case equivalent
reported for a full file lock.
Generally _l_s_o_f can only report on locks held by local processes on
local files. When a local process sets a lock on a remotely mounted
(e.g., NFS) file, the remote server host usually records the lock
state. One exception is Solaris - at some patch levels of 2.3, and in
all versions above 2.4, the Solaris kernel records information on
remote locks in local structures.
_L_s_o_f has trouble reporting locks for some UNIX dialects. Consult the
BBUUGGSS section of this manual page or the _l_s_o_f FAQ (The FFAAQQ section gives
its location.) for more information.
OOUUTTPPUUTT FFOORR OOTTHHEERR PPRROOGGRRAAMMSS
When the --FF option is specified, _l_s_o_f produces output that is suitable
for processing by another program - e.g, an _a_w_k or _P_e_r_l script, or a C
program.
Each unit of information is output in a field that is identified with a
leading character and terminated by a NL (012) (or a NUL (000) if the 0
(zero) field identifier character is specified.) The data of the field
follows immediately after the field identification character and
extends to the field terminator.
It is possible to think of field output as process and file sets. A
process set begins with a field whose identifier is `p' (for process
IDentifier (PID)). It extends to the beginning of the next PID field
or the beginning of the first file set of the process, whichever comes
first. Included in the process set are fields that identify the com‐
mand, the process group IDentification (PGID) number, the task (thread)
ID (TID), and the user ID (UID) number or login name.
A file set begins with a field whose identifier is `f' (for file
descriptor). It is followed by lines that describe the file's access
mode, lock state, type, device, size, offset, inode, protocol, name and
stream module names. It extends to the beginning of the next file or
process set, whichever comes first.
When the NUL (000) field terminator has been selected with the 0 (zero)
field identifier character, _l_s_o_f ends each process and file set with a
NL (012) character.
_L_s_o_f always produces one field, the PID (`p') field. All other fields
may be declared optionally in the field identifier character list that
follows the --FF option. When a field selection character identifies an
item _l_s_o_f does not normally list - e.g., PPID, selected with --RR - spec‐
ification of the field character - e.g., ``--FFRR'' - also selects the
listing of the item.
It is entirely possible to select a set of fields that cannot easily be
parsed - e.g., if the field descriptor field is not selected, it may be
difficult to identify file sets. To help you avoid this difficulty,
_l_s_o_f supports the --FF option; it selects the output of all fields with
NL terminators (the --FF00 option pair selects the output of all fields
with NUL terminators). For compatibility reasons neither --FF nor --FF00
select the raw device field.
These are the fields that _l_s_o_f will produce. The single character
listed first is the field identifier.
a file access mode
c process command name (all characters from proc or
user structure)
C file structure share count
d file's device character code
D file's major/minor device number (0x<hexadecimal>)
f file descriptor (always selected)
F file structure address (0x<hexadecimal>)
G file flaGs (0x<hexadecimal>; names if ++ffgg follows)
g process group ID
i file's inode number
K tasK ID
k link count
l file's lock status
L process login name
m marker between repeated output
n file name, comment, Internet address
N node identifier (ox<hexadecimal>
o file's offset (decimal)
p process ID (always selected)
P protocol name
r raw device number (0x<hexadecimal>)
R parent process ID
s file's size (decimal)
S file's stream identification
t file's type
T TCP/TPI information, identified by prefixes (the
`=' is part of the prefix):
QR=<read queue size>
QS=<send queue size>
SO=<socket options and values> (not all dialects)
SS=<socket states> (not all dialects)
ST=<connection state>
TF=<TCP flags and values> (not all dialects)
WR=<window read size> (not all dialects)
WW=<window write size> (not all dialects)
(TCP/TPI information isn't reported for all supported
UNIX dialects. The --hh or --?? help output for the
--TT option will show what TCP/TPI reporting can be
requested.)
u process user ID
z Solaris 10 and higher zone name
Z SELinux security context (inhibited when SELinux is disabled)
0 use NUL field terminator character in place of NL
1-9 dialect-specific field identifiers (The output
of --FF?? identifies the information to be found
in dialect-specific fields.)
You can get on-line help information on these characters and their
descriptions by specifying the --FF?? option pair. (Escape the `?' char‐
acter as your shell requires.) Additional information on field content
can be found in the OOUUTTPPUUTT section.
As an example, ``--FF ppccffnn'' will select the process ID (`p'), command
name (`c'), file descriptor (`f') and file name (`n') fields with an NL
field terminator character; ``--FF ppccffnn00'' selects the same output with a
NUL (000) field terminator character.
_L_s_o_f doesn't produce all fields for every process or file set, only
those that are available. Some fields are mutually exclusive: file
device characters and file major/minor device numbers; file inode num‐
ber and protocol name; file name and stream identification; file size
and offset. One or the other member of these mutually exclusive sets
will appear in field output, but not both.
Normally _l_s_o_f ends each field with a NL (012) character. The 0 (zero)
field identifier character may be specified to change the field termi‐
nator character to a NUL (000). A NUL terminator may be easier to
process with _x_a_r_g_s _(_1_)_, for example, or with programs whose quoting
mechanisms may not easily cope with the range of characters in the
field output. When the NUL field terminator is in use, _l_s_o_f ends each
process and file set with a NL (012).
Three aids to producing programs that can process _l_s_o_f field output are
included in the _l_s_o_f distribution. The first is a C header file,
_l_s_o_f___f_i_e_l_d_s_._h, that contains symbols for the field identification char‐
acters, indexes for storing them in a table, and explanation strings
that may be compiled into programs. _L_s_o_f uses this header file.
The second aid is a set of sample scripts that process field output,
written in _a_w_k, _P_e_r_l 4, and _P_e_r_l 5. They're located in the _s_c_r_i_p_t_s
subdirectory of the _l_s_o_f distribution.
The third aid is the C library used for the _l_s_o_f test suite. The test
suite is written in C and uses field output to validate the correct
operation of _l_s_o_f. The library can be found in the _t_e_s_t_s_/_L_T_l_i_b_._c file
of the _l_s_o_f distribution. The library uses the first aid, the
_l_s_o_f___f_i_e_l_d_s_._h header file.
BBLLOOCCKKSS AANNDD TTIIMMEEOOUUTTSS
_L_s_o_f can be blocked by some kernel functions that it uses - _l_s_t_a_t(2),
_r_e_a_d_l_i_n_k(2), and _s_t_a_t(2). These functions are stalled in the kernel,
for example, when the hosts where mounted NFS file systems reside
become inaccessible.
_L_s_o_f attempts to break these blocks with timers and child processes,
but the techniques are not wholly reliable. When _l_s_o_f does manage to
break a block, it will report the break with an error message. The
messages may be suppressed with the --tt and --ww options.
The default timeout value may be displayed with the --hh or --?? option,
and it may be changed with the --SS _[_t_] option. The minimum for _t is two
seconds, but you should avoid small values, since slow system respon‐
siveness can cause short timeouts to expire unexpectedly and perhaps
stop _l_s_o_f before it can produce any output.
When _l_s_o_f has to break a block during its access of mounted file system
information, it normally continues, although with less information
available to display about open files.
_L_s_o_f can also be directed to avoid the protection of timers and child
processes when using the kernel functions that might block by specify‐
ing the --OO option. While this will allow _l_s_o_f to start up with less
overhead, it exposes _l_s_o_f completely to the kernel situations that
might block it. Use this option cautiously.
AAVVOOIIDDIINNGG KKEERRNNEELL BBLLOOCCKKSS
You can use the --bb option to tell _l_s_o_f to avoid using kernel functions
that would block. Some cautions apply.
First, using this option usually requires that your system supply
alternate device numbers in place of the device numbers that _l_s_o_f would
normally obtain with the _l_s_t_a_t(2) and _s_t_a_t(2) kernel functions. See
the AALLTTEERRNNAATTEE DDEEVVIICCEE NNUUMMBBEERRSS section for more information on alternate
device numbers.
Second, you can't specify _n_a_m_e_s for _l_s_o_f to locate unless they're file
system names. This is because _l_s_o_f needs to know the device and inode
numbers of files listed with _n_a_m_e_s in the _l_s_o_f options, and the --bb
option prevents _l_s_o_f from obtaining them. Moreover, since _l_s_o_f only
has device numbers for the file systems that have alternates, its abil‐
ity to locate files on file systems depends completely on the avail‐
ability and accuracy of the alternates. If no alternates are avail‐
able, or if they're incorrect, _l_s_o_f won't be able to locate files on
the named file systems.
Third, if the names of your file system directories that _l_s_o_f obtains
from your system's mount table are symbolic links, _l_s_o_f won't be able
to resolve the links. This is because the --bb option causes _l_s_o_f to
avoid the kernel _r_e_a_d_l_i_n_k(2) function it uses to resolve symbolic
links.
Finally, using the --bb option causes _l_s_o_f to issue warning messages when
it needs to use the kernel functions that the --bb option directs it to
avoid. You can suppress these messages by specifying the --ww option,
but if you do, you won't see the alternate device numbers reported in
the warning messages.
AALLTTEERRNNAATTEE DDEEVVIICCEE NNUUMMBBEERRSS
On some dialects, when _l_s_o_f has to break a block because it can't get
information about a mounted file system via the _l_s_t_a_t(2) and _s_t_a_t(2)
kernel functions, or because you specified the --bb option, _l_s_o_f can
obtain some of the information it needs - the device number and possi‐
bly the file system type - from the system mount table. When that is
possible, _l_s_o_f will report the device number it obtained. (You can
suppress the report by specifying the --ww option.)
You can assist this process if your mount table is supported with an
_/_e_t_c_/_m_t_a_b or _/_e_t_c_/_m_n_t_t_a_b file that contains an options field by adding
a ``dev=xxxx'' field for mount points that do not have one in their
options strings. Note: you must be able to edit the file - i.e., some
mount tables like recent Solaris /etc/mnttab or Linux /proc/mounts are
read-only and can't be modified.
You may also be able to supply device numbers using the ++mm and ++mm _m
options, provided they are supported by your dialect. Check the output
of _l_s_o_f_'_s --hh or --?? options to see if the ++mm and ++mm _m options are
available.
The ``xxxx'' portion of the field is the hexadecimal value of the file
system's device number. (Consult the _s_t___d_e_v field of the output of the
_l_s_t_a_t(2) and _s_t_a_t(2) functions for the appropriate values for your file
systems.) Here's an example from a Sun Solaris 2.6 _/_e_t_c_/_m_n_t_t_a_b for a
file system remotely mounted via NFS:
nfs ignore,noquota,dev=2a40001
There's an advantage to having ``dev=xxxx'' entries in your mount table
file, especially for file systems that are mounted from remote NFS
servers. When a remote server crashes and you want to identify its
users by running _l_s_o_f on one of its clients, _l_s_o_f probably won't be
able to get output from the _l_s_t_a_t(2) and _s_t_a_t(2) functions for the file
system. If it can obtain the file system's device number from the
mount table, it will be able to display the files open on the crashed
NFS server.
Some dialects that do not use an ASCII _/_e_t_c_/_m_t_a_b or _/_e_t_c_/_m_n_t_t_a_b file
for the mount table may still provide an alternative device number in
their internal mount tables. This includes AIX, Apple Darwin, FreeBSD,
NetBSD, OpenBSD, and Tru64 UNIX. _L_s_o_f knows how to obtain the alterna‐
tive device number for these dialects and uses it when its attempt to
_l_s_t_a_t(2) or _s_t_a_t(2) the file system is blocked.
If you're not sure your dialect supplies alternate device numbers for
file systems from its mount table, use this _l_s_o_f incantation to see if
it reports any alternate device numbers:
lsof -b
Look for standard error file warning messages that begin ``assuming
"dev=xxxx" from ...''.
KKEERRNNEELL NNAAMMEE CCAACCHHEE
_L_s_o_f is able to examine the kernel's name cache or use other kernel
facilities (e.g., the ADVFS 4.x tag_to_path() function under Tru64
UNIX) on some dialects for most file system types, excluding AFS, and
extract recently used path name components from it. (AFS file system
path lookups don't use the kernel's name cache; some Solaris VxFS file
system operations apparently don't use it, either.)
_L_s_o_f reports the complete paths it finds in the NAME column. If _l_s_o_f
can't report all components in a path, it reports in the NAME column
the file system name, followed by a space, two `-' characters, another
space, and the name components it has located, separated by the `/'
character.
When _l_s_o_f is run in repeat mode - i.e., with the --rr option specified -
the extent to which it can report path name components for the same
file may vary from cycle to cycle. That's because other running pro‐
cesses can cause the kernel to remove entries from its name cache and
replace them with others.
_L_s_o_f_'_s use of the kernel name cache to identify the paths of files can
lead it to report incorrect components under some circumstances. This
can happen when the kernel name cache uses device and node number as a
key (e.g., SCO OpenServer) and a key on a rapidly changing file system
is reused. If the UNIX dialect's kernel doesn't purge the name cache
entry for a file when it is unlinked, _l_s_o_f may find a reference to the
wrong entry in the cache. The _l_s_o_f FAQ (The FFAAQQ section gives its
location.) has more information on this situation.
_L_s_o_f can report path name components for these dialects:
FreeBSD
HP-UX
Linux
NetBSD
NEXTSTEP
OpenBSD
OPENSTEP
SCO OpenServer
SCO|Caldera UnixWare
Solaris
Tru64 UNIX
_L_s_o_f can't report path name components for these dialects:
AIX
If you want to know why _l_s_o_f can't report path name components for some
dialects, see the _l_s_o_f FAQ (The FFAAQQ section gives its location.)
DDEEVVIICCEE CCAACCHHEE FFIILLEE
Examining all members of the _/_d_e_v (or _/_d_e_v_i_c_e_s) node tree with _s_t_a_t(2)
functions can be time consuming. What's more, the information that
_l_s_o_f needs - device number, inode number, and path - rarely changes.
Consequently, _l_s_o_f normally maintains an ASCII text file of cached _/_d_e_v
(or _/_d_e_v_i_c_e_s) information (exception: the /proc-based Linux _l_s_o_f where
it's not needed.) The local system administrator who builds _l_s_o_f can
control the way the device cache file path is formed, selecting from
these options:
Path from the --DD option;
Path from an environment variable;
System-wide path;
Personal path (the default);
Personal path, modified by an environment variable.
Consult the output of the --hh, --DD?? ,, or --?? help options for the current
state of device cache support. The help output lists the default
read-mode device cache file path that is in effect for the current
invocation of _l_s_o_f. The --DD?? option output lists the read-only and
write device cache file paths, the names of any applicable environment
variables, and the personal device cache path format.
_L_s_o_f can detect that the current device cache file has been acciden‐
tally or maliciously modified by integrity checks, including the compu‐
tation and verification of a sixteen bit Cyclic Redundancy Check (CRC)
sum on the file's contents. When _l_s_o_f senses something wrong with the
file, it issues a warning and attempts to remove the current cache file
and create a new copy, but only to a path that the process can legiti‐
mately write.
The path from which a _l_s_o_f process may attempt to read a device cache
file may not be the same as the path to which it can legitimately
write. Thus when _l_s_o_f senses that it needs to update the device cache
file, it may choose a different path for writing it from the path from
which it read an incorrect or outdated version.
If available, the --DDrr option will inhibit the writing of a new device
cache file. (It's always available when specified without a path name
argument.)
When a new device is added to the system, the device cache file may
need to be recreated. Since _l_s_o_f compares the mtime of the device
cache file with the mtime and ctime of the _/_d_e_v (or _/_d_e_v_i_c_e_s) direc‐
tory, it usually detects that a new device has been added; in that case
_l_s_o_f issues a warning message and attempts to rebuild the device cache
file.
Whenever _l_s_o_f writes a device cache file, it sets its ownership to the
real UID of the executing process, and its permission modes to 0600,
this restricting its reading and writing to the file's owner.
LLSSOOFF PPEERRMMIISSSSIIOONNSS TTHHAATT AAFFFFEECCTT DDEEVVIICCEE CCAACCHHEE FFIILLEE AACCCCEESSSS
Two permissions of the _l_s_o_f executable affect its ability to access
device cache files. The permissions are set by the local system admin‐
istrator when _l_s_o_f is installed.
The first and rarer permission is setuid-root. It comes into effect
when _l_s_o_f is executed; its effective UID is then root, while its real
(i.e., that of the logged-on user) UID is not. The _l_s_o_f distribution
recommends that versions for these dialects run setuid-root.
HP-UX 11.11 and 11.23
Linux
The second and more common permission is setgid. It comes into effect
when the effective group IDentification number (GID) of the _l_s_o_f
process is set to one that can access kernel memory devices - e.g.,
``kmem'', ``sys'', or ``system''.
An _l_s_o_f process that has setgid permission usually surrenders the per‐
mission after it has accessed the kernel memory devices. When it does
that, _l_s_o_f can allow more liberal device cache path formations. The
_l_s_o_f distribution recommends that versions for these dialects run set‐
gid and be allowed to surrender setgid permission.
AIX 5.[12] and 5.3-ML1
Apple Darwin 7.x Power Macintosh systems
FreeBSD 4.x, 4.1x, 5.x and [6789].x for x86-based systems
FreeBSD 5.x and [6789].x for Alpha, AMD64 and Sparc64-based
systems
HP-UX 11.00
NetBSD 1.[456], 2.x and 3.x for Alpha, x86, and SPARC-based
systems
NEXTSTEP 3.[13] for NEXTSTEP architectures
OpenBSD 2.[89] and 3.[0-9] for x86-based systems
OPENSTEP 4.x
SCO OpenServer Release 5.0.6 for x86-based systems
SCO|Caldera UnixWare 7.1.4 for x86-based systems
Solaris 2.6, 8, 9 and 10
Tru64 UNIX 5.1
(Note: _l_s_o_f for AIX 5L and above needs setuid-root permission if its --XX
option is used.)
_L_s_o_f for these dialects does not support a device cache, so the permis‐
sions given to the executable don't apply to the device cache file.
Linux
DDEEVVIICCEE CCAACCHHEE FFIILLEE PPAATTHH FFRROOMM TTHHEE --DD OOPPTTIIOONN
The --DD option provides limited means for specifying the device cache
file path. Its ?? function will report the read-only and write device
cache file paths that _l_s_o_f will use.
When the --DD bb, rr, and uu functions are available, you can use them to
request that the cache file be built in a specific location (bb[_p_a_t_h]);
read but not rebuilt (rr[_p_a_t_h]); or read and rebuilt (uu[_p_a_t_h]). The bb,
rr, and uu functions are restricted under some conditions. They are
restricted when the _l_s_o_f process is setuid-root. The path specified
with the rr function is always read-only, even when it is available.
The bb, rr, and uu functions are also restricted when the _l_s_o_f process
runs setgid and _l_s_o_f doesn't surrender the setgid permission. (See the
LLSSOOFF PPEERRMMIISSSSIIOONNSS TTHHAATT AAFFFFEECCTT DDEEVVIICCEE CCAACCHHEE FFIILLEE AACCCCEESSSS section for a
list of implementations that normally don't surrender their setgid per‐
mission.)
A further --DD function, ii (for ignore), is always available.
When available, the bb function tells _l_s_o_f to read device information
from the kernel with the _s_t_a_t(2) function and build a device cache file
at the indicated path.
When available, the rr function tells _l_s_o_f to read the device cache
file, but not update it. When a path argument accompanies --DDrr, it
names the device cache file path. The rr function is always available
when it is specified without a path name argument. If _l_s_o_f is not run‐
ning setuid-root and surrenders its setgid permission, a path name
argument may accompany the rr function.
When available, the uu function tells _l_s_o_f to attempt to read and use
the device cache file. If it can't read the file, or if it finds the
contents of the file incorrect or outdated, it will read information
from the kernel, and attempt to write an updated version of the device
cache file, but only to a path it considers legitimate for the _l_s_o_f
process effective and real UIDs.
DDEEVVIICCEE CCAACCHHEE PPAATTHH FFRROOMM AANN EENNVVIIRROONNMMEENNTT VVAARRIIAABBLLEE
_L_s_o_f_'_s second choice for the device cache file is the contents of the
LSOFDEVCACHE environment variable. It avoids this choice if the _l_s_o_f
process is setuid-root, or the real UID of the process is root.
A further restriction applies to a device cache file path taken from
the LSOFDEVCACHE environment variable: _l_s_o_f will not write a device
cache file to the path if the _l_s_o_f process doesn't surrender its setgid
permission. (See the LLSSOOFF PPEERRMMIISSSSIIOONNSS TTHHAATT AAFFFFEECCTT DDEEVVIICCEE CCAACCHHEE FFIILLEE
AACCCCEESSSS section for information on implementations that don't surrender
their setgid permission.)
The local system administrator can disable the use of the LSOFDEVCACHE
environment variable or change its name when building _l_s_o_f. Consult
the output of --DD?? for the environment variable's name.
SSYYSSTTEEMM--WWIIDDEE DDEEVVIICCEE CCAACCHHEE PPAATTHH
The local system administrator may choose to have a system-wide device
cache file when building _l_s_o_f. That file will generally be constructed
by a special system administration procedure when the system is booted
or when the contents of _/_d_e_v or _/_d_e_v_i_c_e_s) changes. If defined, it is
_l_s_o_f_'_s third device cache file path choice.
You can tell that a system-wide device cache file is in effect for your
local installation by examining the _l_s_o_f help option output - i.e., the
output from the --hh or --?? option.
_L_s_o_f will never write to the system-wide device cache file path by
default. It must be explicitly named with a --DD function in a
root-owned procedure. Once the file has been written, the procedure
must change its permission modes to 0644 (owner-read and owner-write,
group-read, and other-read).
PPEERRSSOONNAALL DDEEVVIICCEE CCAACCHHEE PPAATTHH ((DDEEFFAAUULLTT))
The default device cache file path of the _l_s_o_f distribution is one
recorded in the home directory of the real UID that executes _l_s_o_f.
Added to the home directory is a second path component of the form
_._l_s_o_f___h_o_s_t_n_a_m_e.
This is _l_s_o_f_'_s fourth device cache file path choice, and is usually the
default. If a system-wide device cache file path was defined when _l_s_o_f
was built, this fourth choice will be applied when _l_s_o_f can't find the
system-wide device cache file. This is the oonnllyy time _l_s_o_f uses two
paths when reading the device cache file.
The _h_o_s_t_n_a_m_e part of the second component is the base name of the exe‐
cuting host, as returned by _g_e_t_h_o_s_t_n_a_m_e(2). The base name is defined
to be the characters preceding the first `.' in the _g_e_t_h_o_s_t_n_a_m_e(2)
output, or all the _g_e_t_h_o_s_t_n_a_m_e(2) output if it contains no `.'.
The device cache file belongs to the user ID and is readable and
writable by the user ID alone - i.e., its modes are 0600. Each dis‐
tinct real user ID on a given host that executes _l_s_o_f has a distinct
device cache file. The _h_o_s_t_n_a_m_e part of the path distinguishes device
cache files in an NFS-mounted home directory into which device cache
files are written from several different hosts.
The personal device cache file path formed by this method represents a
device cache file that _l_s_o_f will attempt to read, and will attempt to
write should it not exist or should its contents be incorrect or out‐
dated.
The --DDrr option without a path name argument will inhibit the writing of
a new device cache file.
The --DD?? option will list the format specification for constructing the
personal device cache file. The conversions used in the format speci‐
fication are described in the _0_0_D_C_A_C_H_E file of the _l_s_o_f distribution.
MMOODDIIFFIIEEDD PPEERRSSOONNAALL DDEEVVIICCEE CCAACCHHEE PPAATTHH
If this option is defined by the local system administrator when _l_s_o_f
is built, the LSOFPERSDCPATH environment variable contents may be used
to add a component of the personal device cache file path.
The LSOFPERSDCPATH variable contents are inserted in the path at the
place marked by the local system administrator with the ``%p'' conver‐
sion in the HASPERSDC format specification of the dialect's _m_a_c_h_i_n_e_._h
header file. (It's placed right after the home directory in the
default _l_s_o_f distribution.)
Thus, for example, if LSOFPERSDCPATH contains ``LSOF'', the home direc‐
tory is ``/Homes/abe'', the host name is ``lsof.itap.purdue.edu'', and
the HASPERSDC format is the default (``%h/%p.lsof_%L''), the modified
personal device cache file path is:
/Homes/abe/LSOF/.lsof_vic
The LSOFPERSDCPATH environment variable is ignored when the _l_s_o_f
process is setuid-root or when the real UID of the process is root.
_L_s_o_f will not write to a modified personal device cache file path if
the _l_s_o_f process doesn't surrender setgid permission. (See the LLSSOOFF
PPEERRMMIISSSSIIOONNSS TTHHAATT AAFFFFEECCTT DDEEVVIICCEE CCAACCHHEE FFIILLEE AACCCCEESSSS section for a list of
implementations that normally don't surrender their setgid permission.)
If, for example, you want to create a sub-directory of personal device
cache file paths by using the LSOFPERSDCPATH environment variable to
name it, and _l_s_o_f doesn't surrender its setgid permission, you will
have to allow _l_s_o_f to create device cache files at the standard per‐
sonal path and move them to your subdirectory with shell commands.
The local system administrator may: disable this option when _l_s_o_f is
built; change the name of the environment variable from LSOFPERSDCPATH
to something else; change the HASPERSDC format to include the personal
path component in another place; or exclude the personal path component
entirely. Consult the output of the --DD?? option for the environment
variable's name and the HASPERSDC format specification.
DDIIAAGGNNOOSSTTIICCSS
Errors are identified with messages on the standard error file.
_L_s_o_f returns a one (1) if any error was detected, including the failure
to locate command names, file names, Internet addresses or files, login
names, NFS files, PIDs, PGIDs, or UIDs it was asked to list. If the --VV
option is specified, _l_s_o_f will indicate the search items it failed to
list.
It returns a zero (0) if no errors were detected and if it was able to
list some information about all the specified search arguments.
When _l_s_o_f cannot open access to _/_d_e_v (or _/_d_e_v_i_c_e_s) or one of its subdi‐
rectories, or get information on a file in them with _s_t_a_t(2), it issues
a warning message and continues. That _l_s_o_f will issue warning messages
about inaccessible files in _/_d_e_v (or _/_d_e_v_i_c_e_s) is indicated in its help
output - requested with the --hh or >B -? options - with the message:
Inaccessible /dev warnings are enabled.
The warning message may be suppressed with the --ww option. It may also
have been suppressed by the system administrator when _l_s_o_f was compiled
by the setting of the WARNDEVACCESS definition. In this case, the out‐
put from the help options will include the message:
Inaccessible /dev warnings are disabled.
Inaccessible device warning messages usually disappear after _l_s_o_f has
created a working device cache file.
EEXXAAMMPPLLEESS
For a more extensive set of examples, documented more fully, see the
_0_0_Q_U_I_C_K_S_T_A_R_T file of the _l_s_o_f distribution.
To list all open files, use:
lsof
To list all open Internet, x.25 (HP-UX), and UNIX domain files, use:
lsof -i -U
To list all open IPv4 network files in use by the process whose PID is
1234, use:
lsof -i 4 -a -p 1234
Presuming the UNIX dialect supports IPv6, to list only open IPv6 net‐
work files, use:
lsof -i 6
To list all files using any protocol on ports 513, 514, or 515 of host
wonderland.cc.purdue.edu, use:
lsof -i @wonderland.cc.purdue.edu:513-515
To list all files using any protocol on any port of mace.cc.purdue.edu
(cc.purdue.edu is the default domain), use:
lsof -i @mace
To list all open files for login name ``abe'', or user ID 1234, or
process 456, or process 123, or process 789, use:
lsof -p 456,123,789 -u 1234,abe
To list all open files on device /dev/hd4, use:
lsof /dev/hd4
To find the process that has /u/abe/foo open, use:
lsof /u/abe/foo
To send a SIGHUP to the processes that have /u/abe/bar open, use:
kill -HUP `lsof -t /u/abe/bar`
To find any open file, including an open UNIX domain socket file, with
the name _/_d_e_v_/_l_o_g, use:
lsof /dev/log
To find processes with open files on the NFS file system named
_/_n_f_s_/_m_o_u_n_t_/_p_o_i_n_t whose server is inaccessible, and presuming your mount
table supplies the device number for _/_n_f_s_/_m_o_u_n_t_/_p_o_i_n_t, use:
lsof -b /nfs/mount/point
To do the preceding search with warning messages suppressed, use:
lsof -bw /nfs/mount/point
To ignore the device cache file, use:
lsof -Di
To obtain PID and command name field output for each process, file
descriptor, file device number, and file inode number for each file of
each process, use:
lsof -FpcfDi
To list the files at descriptors 1 and 3 of every process running the
_l_s_o_f command for login ID ``abe'' every 10 seconds, use:
lsof -c lsof -a -d 1 -d 3 -u abe -r10
To list the current working directory of processes running a command
that is exactly four characters long and has an 'o' or 'O' in character
three, use this regular expression form of the --cc _c option:
lsof -c /^..o.$/i -a -d cwd
To find an IP version 4 socket file by its associated numeric dot-form
address, use:
lsof -i@128.210.15.17
To find an IP version 6 socket file (when the UNIX dialect supports
IPv6) by its associated numeric colon-form address, use:
lsof -i@[0:1:2:3:4:5:6:7]
To find an IP version 6 socket file (when the UNIX dialect supports
IPv6) by an associated numeric colon-form address that has a run of
zeroes in it - e.g., the loop-back address - use:
lsof -i@[::1]
To obtain a repeat mode marker line that contains the current time,
use:
lsof -rm====%T====
To add spaces to the previous marker line, use:
lsof -r "m==== %T ===="
BBUUGGSS
Since _l_s_o_f reads kernel memory in its search for open files, rapid
changes in kernel memory may produce unpredictable results.
When a file has multiple record locks, the lock status character (fol‐
lowing the file descriptor) is derived from a test of the first lock
structure, not from any combination of the individual record locks that
might be described by multiple lock structures.
_L_s_o_f can't search for files with restrictive access permissions by _n_a_m_e
unless it is installed with root set-UID permission. Otherwise it is
limited to searching for files to which its user or its set-GID group
(if any) has access permission.
The display of the destination address of a raw socket (e.g., for _p_i_n_g)
depends on the UNIX operating system. Some dialects store the destina‐
tion address in the raw socket's protocol control block, some do not.
_L_s_o_f can't always represent Solaris device numbers in the same way that
_l_s(1) does. For example, the major and minor device numbers that the
_l_s_t_a_t(2) and _s_t_a_t(2) functions report for the directory on which CD-ROM
files are mounted (typically _/_c_d_r_o_m) are not the same as the ones that
it reports for the device on which CD-ROM files are mounted (typically
_/_d_e_v_/_s_r_0). (_L_s_o_f reports the directory numbers.)
The support for _/_p_r_o_c file systems is available only for BSD and Tru64
UNIX dialects, Linux, and dialects derived from SYSV R4 - e.g., Free‐
BSD, NetBSD, OpenBSD, Solaris, UnixWare.
Some _/_p_r_o_c file items - device number, inode number, and file size -
are unavailable in some dialects. Searching for files in a _/_p_r_o_c file
system may require that the full path name be specified.
No text (ttxxtt) file descriptors are displayed for Linux processes. All
entries for files other than the current working directory, the root
directory, and numerical file descriptors are labeled mmeemm descriptors.
_L_s_o_f can't search for Tru64 UNIX named pipes by name, because their
kernel implementation of lstat(2) returns an improper device number for
a named pipe.
_L_s_o_f can't report fully or correctly on HP-UX 9.01, 10.20, and 11.00
locks because of insufficient access to kernel data or errors in the
kernel data. See the _l_s_o_f FAQ (The FFAAQQ section gives its location.)
for details.
The AIX SMT file type is a fabrication. It's made up for file struc‐
tures whose type (15) isn't defined in the AIX _/_u_s_r_/_i_n_c_l_u_d_e_/_s_y_s_/_f_i_l_e_._h
header file. One way to create such file structures is to run X
clients with the DISPLAY variable set to ``:0.0''.
The ++||--ff_[_c_f_g_G_n_] option is not supported under /proc-based Linux _l_s_o_f,
because it doesn't read kernel structures from kernel memory.
EENNVVIIRROONNMMEENNTT
_L_s_o_f may access these environment variables.
LANG defines a language locale. See _s_e_t_l_o_c_a_l_e(3) for the
names of other variables that can be used in place of
LANG - e.g., LC_ALL, LC_TYPE, etc.
LSOFDEVCACHE defines the path to a device cache file. See the
DDEEVVIICCEE CCAACCHHEE PPAATTHH FFRROOMM AANN EENNVVIIRROONNMMEENNTT VVAARRIIAABBLLEE sec‐
tion for more information.
LSOFPERSDCPATH defines the middle component of a modified personal
device cache file path. See the MMOODDIIFFIIEEDD PPEERRSSOONNAALL
DDEEVVIICCEE CCAACCHHEE PPAATTHH section for more information.
FFAAQQ
Frequently-asked questions and their answers (an FAQ) are available in
the _0_0_F_A_Q file of the _l_s_o_f distribution.
That file is also available via anonymous ftp from _l_s_o_f_._i_t_a_p_._p_u_r_d_u_e_._e_d_u
at _p_u_b_/_t_o_o_l_s_/_u_n_i_x_/_l_s_o_fFAQ_. The URL is:
ftp://lsof.itap.purdue.edu/pub/tools/unix/lsof/FAQ
FFIILLEESS
_/_d_e_v_/_k_m_e_m kernel virtual memory device
_/_d_e_v_/_m_e_m physical memory device
_/_d_e_v_/_s_w_a_p system paging device
_._l_s_o_f___h_o_s_t_n_a_m_e _l_s_o_f_'_s device cache file (The suffix, _h_o_s_t_n_a_m_e, is
the first component of the host's name returned by
_g_e_t_h_o_s_t_n_a_m_e(2).)
AAUUTTHHOORRSS
_L_s_o_f was written by Victor A.Abell <abe@purdue.edu> of Purdue Univer‐
sity. Many others have contributed to _l_s_o_f. They're listed in the
_0_0_C_R_E_D_I_T_S file of the _l_s_o_f distribution.
DDIISSTTRRIIBBUUTTIIOONN
The latest distribution of _l_s_o_f is available via anonymous ftp from the
host _l_s_o_f_._i_t_a_p_._p_u_r_d_u_e_._e_d_u. You'll find the _l_s_o_f distribution in the
_p_u_b_/_t_o_o_l_s_/_u_n_i_x_/_l_s_o_f directory.
You can also use this URL:
ftp://lsof.itap.purdue.edu/pub/tools/unix/lsof
_L_s_o_f is also mirrored elsewhere. When you access _l_s_o_f_._i_t_a_p_._p_u_r_d_u_e_._e_d_u
and change to its _p_u_b_/_t_o_o_l_s_/_u_n_i_x_/_l_s_o_f directory, you'll be given a list
of some mirror sites. The _p_u_b_/_t_o_o_l_s_/_u_n_i_x_/_l_s_o_f directory also contains
a more complete list in its _m_i_r_r_o_r_s file. Use mirrors with caution -
not all mirrors always have the latest _l_s_o_f revision.
Some pre-compiled _L_s_o_f executables are available on _l_s_o_f_._i_t_a_p_._p_u_r_‐
_d_u_e_._e_d_u, but their use is discouraged - it's better that you build your
own from the sources. If you feel you must use a pre-compiled exe‐
cutable, please read the cautions that appear in the README files of
the _p_u_b_/_t_o_o_l_s_/_u_n_i_x_/_l_s_o_f_/_b_i_n_a_r_i_e_s subdirectories and in the 00* files of
the distribution.
More information on the _l_s_o_f distribution can be found in its
_R_E_A_D_M_E_._l_s_o_f___<_v_e_r_s_i_o_n_> file. If you intend to get the _l_s_o_f distribution
and build it, please read _R_E_A_D_M_E_._l_s_o_f___<_v_e_r_s_i_o_n_> and the other 00* files
of the distribution before sending questions to the author.
SSEEEE AALLSSOO
Not all the following manual pages may exist in every UNIX dialect to
which _l_s_o_f has been ported.
access(2), awk(1), crash(1), fattach(3C), ff(1), fstat(8), fuser(1),
gethostname(2), isprint(3), kill(1), localtime(3), lstat(2), mod‐
load(8), mount(8), netstat(1), ofiles(8L), perl(1), ps(1), readlink(2),
setlocale(3), stat(2), strftime(3), time(2), uname(1).
Revision-4.89 LSOF(8)
importlib.reload(cdt_reader)
hello,world
<module 'cdt_reader' from '/home/bms270/BMS270_2018/cdt_reader.py'>
cdt_reader.__file__
'/home/bms270/BMS270_2018/cdt_reader.py'
!ls *.pyc
ls: cannot access '*.pyc': No such file or directory
(colnames,genes,annotations,data2) = cdt_reader.parse_cdt("supp2data.cdt",0.)
data2[0][:10]
[0.33, -0.17, 0.04, -0.07, -0.09, -0.12, -0.03, -0.2, -0.06, -0.06]
small_data2 = data2[:10]
import stats
stats.pearson(small_data2[0],small_data2[1])
0.12164363213592637
%time
print("hi")
print("there")
CPU times: user 0 ns, sys: 0 ns, total: 0 ns Wall time: 6.2 µs hi there
for i in small_data2:
print(i)
break
[0.33, -0.17, 0.04, -0.07, -0.09, -0.12, -0.03, -0.2, -0.06, -0.06, -0.14, -0.18, -0.06, -0.25, 0.06, -0.12, 0.25, 0.43, 0.21, -0.04, -0.15, -0.04, 0.21, -0.14, -0.03, -0.07, -0.36, -0.14, -0.42, -0.34, -0.23, -0.17, 0.23, 0.3, 0.41, -0.07, -0.23, -0.12, 0.16, 0.74, 0.14, -0.49, -0.32, 0.19, 0.23, 0.24, 0.28, 1.13, -0.12, 0.1, 0.0, 0.66, 0.62, 0.08, 0.62, 0.43, 0.5, -0.25, -0.51, -0.67, 0.21, -0.74, -0.36, -0.01, 0.38, 0.15, -0.22, -0.09, 0.33, 0.08, 0.39, -0.17, 0.23, 0.2, 0.2, -0.17, -0.69, 0.14, -0.27]
fp = open("myfile.txt","w")
fp.write("Hello, world")
12
fp.write("A second line")
13
fp.close()
print(open("myfile.txt").read())
Hello, worldA second line
fp = open("myfile.txt","w")
fp.write("Hello, world\n")
fp.write("A second line\n")
fp.close()
print(open("myfile.txt").read())
Hello, world A second line
open("myfile.txt").read()
'Hello, world\nA second line\n'
fp = open("myfile.txt","w")
fp.write("Some log text")
fp.flush()
open("myfile.txt").read()
'Some log text'
fp.close()
"\t".join(["hello","world"])
'hello\tworld'
"\t".join([1,2,3])
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-43-d6d3ec56d3d0> in <module>() ----> 1 "\t".join([1,2,3]) TypeError: sequence item 0: expected str instance, int found
s = []
for i in [1,2,3]:
s.append(str(i))
"\t".join(s)
'1\t2\t3'
from csv import reader,writer,excel_tab
fin = reader(open("supp2data.cdt"), dialect=excel_tab)
for i in fin:
print(i)
break
['ORF', 'NAME', 'alpha 0', 'alpha 7', 'alpha 14', 'alpha 21', 'alpha 28', 'alpha 35', 'alpha 42', 'alpha 49', 'alpha 56', 'alpha 63', 'alpha 70', 'alpha 77', 'alpha 84', 'alpha 91', 'alpha 98', 'alpha 105', 'alpha 112', 'alpha 119', 'Elu 0', 'Elu 30', 'Elu 60', 'Elu 90', 'Elu 120', 'Elu 150', 'Elu 180', 'Elu 210', 'Elu 240', 'Elu 270', 'Elu 300', 'Elu 330', 'Elu 360', 'Elu 390', 'cdc15 10', 'cdc15 30', 'cdc15 50', 'cdc15 70', 'cdc15 90', 'cdc15 110', 'cdc15 130', 'cdc15 150', 'cdc15 170', 'cdc15 190', 'cdc15 210', 'cdc15 230', 'cdc15 250', 'cdc15 270', 'cdc15 290', 'spo 0', 'spo 2', 'spo 5', 'spo 7', 'spo 9', 'spo 11', 'spo5 2', 'spo5 7', 'spo5 11', 'spo- early', 'spo- mid', 'heat 0', 'heat 10', 'heat 20', 'heat 40', 'heat 80', 'heat 160', 'dtt 15', 'dtt 30', 'dtt 60', 'dtt 120', 'cold 0', 'cold 20', 'cold 40', 'cold 160', 'diau a', 'diau b', 'diau c', 'diau d', 'diau e', 'diau f', 'diau g']
fout = writer(open("example.csv","w"))
for i in small_data2:
fout.writerow(i)
del fout
print(open("example.csv").read())
0.33,-0.17,0.04,-0.07,-0.09,-0.12,-0.03,-0.2,-0.06,-0.06,-0.14,-0.18,-0.06,-0.25,0.06,-0.12,0.25,0.43,0.21,-0.04,-0.15,-0.04,0.21,-0.14,-0.03,-0.07,-0.36,-0.14,-0.42,-0.34,-0.23,-0.17,0.23,0.3,0.41,-0.07,-0.23,-0.12,0.16,0.74,0.14,-0.49,-0.32,0.19,0.23,0.24,0.28,1.13,-0.12,0.1,0.0,0.66,0.62,0.08,0.62,0.43,0.5,-0.25,-0.51,-0.67,0.21,-0.74,-0.36,-0.01,0.38,0.15,-0.22,-0.09,0.33,0.08,0.39,-0.17,0.23,0.2,0.2,-0.17,-0.69,0.14,-0.27 -0.64,-0.38,-0.32,-0.29,-0.22,-0.01,-0.32,-0.27,-0.51,-0.67,-0.62,-0.58,-0.38,-0.94,-0.34,-0.92,-0.15,0.03,0.16,-0.34,-0.32,-0.34,-0.12,-0.34,-0.27,-0.15,-0.15,-0.51,-0.3,-0.25,-0.12,-0.4,0.98,0.99,0.25,0.15,0.08,0.23,0.18,-0.29,-0.45,0.01,-0.34,-1.12,-0.54,-0.94,-1.09,-0.45,-0.23,-0.36,0.08,0.28,0.18,-0.12,0.0,0.25,-0.22,-0.04,-0.25,0.04,-0.03,-0.07,-0.04,0.73,-0.06,0.54,-0.09,-0.29,-0.1,0.36,-0.2,-0.34,-0.14,-0.09,0.06,-0.17,0.04,-0.97,-1.79 -0.23,0.19,-0.36,0.14,-0.4,0.16,-0.09,-0.12,-0.14,-0.14,-0.38,-0.22,0.12,-0.43,-0.42,-0.45,-0.17,-0.27,0.29,-0.09,0.4,-0.1,0.46,0.15,-0.17,-0.18,-0.07,-0.34,0.3,-0.12,-0.06,-0.17,0.07,0.38,0.34,0.0,-0.15,-0.2,0.19,0.37,0.24,-0.07,0.0,0.24,0.45,0.23,0.5,-0.07,0.0,0.66,0.94,0.46,0.06,-0.18,0.39,-0.18,0.16,0.55,-0.06,-0.94,0.21,-0.71,-0.86,-0.45,0.42,1.04,0.65,0.53,-0.47,0.21,-0.29,-0.36,-0.1,-0.29,-0.18,-0.34,-0.47,-0.43,-1.06 -0.69,-0.89,-0.74,-0.56,-0.64,-0.18,-0.42,-0.34,0.0,0.01,-0.1,-0.17,-0.12,-0.43,-0.18,0.06,-0.2,-0.22,-0.04,0.34,0.42,-0.04,-0.14,0.15,0.26,0.4,0.24,0.25,0.37,-0.04,-0.27,0.11,-0.15,-0.07,0.06,0.23,0.07,-0.12,-0.12,0.0,0.04,0.25,0.1,0.3,-0.12,-0.23,-0.12,0.19,0.24,0.0,0.41,0.36,0.98,-0.04,0.18,0.24,0.44,0.32,-0.22,-0.71,-0.34,-0.45,-0.3,-0.45,0.58,-0.22,0.1,0.19,-0.32,-0.01,-0.29,0.31,0.21,0.07,0.18,-0.14,-0.2,-0.43,-1.51 0.04,0.01,-0.81,0.0,-0.3,0.49,0.08,0.19,-0.03,-0.32,-0.34,-0.22,-0.03,-0.06,0.06,0.07,0.1,0.03,-0.18,-0.2,-0.12,0.16,-0.17,0.1,-0.14,-0.01,-0.15,0.04,0.23,-0.04,0.07,0.06,0.7,0.36,0.37,0.3,-0.04,0.19,-0.45,0.21,-1.12,-0.04,0.3,0.88,-0.49,-0.23,-0.04,-0.2,0.45,0.52,0.62,0.48,0.65,-0.14,-0.14,-0.49,-0.04,0.14,-0.1,-0.2,0.01,-0.4,-0.23,-0.04,0.25,-0.27,0.1,0.1,-0.2,0.28,-0.17,0.26,0.07,-0.17,0.0,-0.1,-0.23,-0.51,-1.4 0.11,0.32,0.03,0.32,0.03,-0.12,0.01,-0.36,-0.01,-0.17,-0.22,-0.22,-0.1,-0.51,-0.25,-0.38,-0.27,-0.2,-0.45,0.82,-0.12,-0.43,-0.1,-0.1,-0.64,0.08,0.1,0.2,0.2,0.16,0.2,0.2,-0.2,-0.14,0.19,0.15,0.3,0.14,0.0,-0.14,-0.18,0.01,0.03,-0.38,0.2,0.19,0.41,-0.4,-0.07,0.0,0.74,-0.09,0.38,-0.64,-0.04,-0.1,-0.23,-0.56,-0.25,-1.0,-0.25,-0.62,-0.64,-0.36,-0.3,-0.12,0.16,-0.34,-0.17,0.39,-0.06,-0.67,0.04,-0.22,-0.12,-0.15,-0.67,-0.38,-0.27 -0.47,1.0,-0.51,-0.25,-0.71,-0.22,-0.3,-0.36,-0.1,0.08,0.0,-0.27,-0.23,-0.45,-0.32,-0.17,-0.56,-0.01,0.44,0.26,0.4,0.12,-0.03,0.07,0.16,0.58,0.33,0.2,0.14,0.2,0.34,0.21,0.82,0.52,0.48,0.77,0.14,0.55,0.37,0.25,0.29,0.18,0.07,0.73,0.37,-0.01,0.24,0.25,-0.1,0.11,0.21,0.08,0.12,-0.14,0.39,0.28,-0.1,-0.4,0.43,-0.1,-0.01,-0.2,-0.18,-0.1,-0.22,-0.43,-0.17,0.04,-0.06,0.24,-0.04,-0.4,-0.38,-0.56,0.11,-0.27,-0.58,0.48,0.19 -0.25,0.26,0.01,-0.06,-0.42,-0.07,-0.3,-0.18,-0.1,-0.27,-0.29,-0.04,0.04,-0.18,-0.1,-0.03,-0.4,0.03,0.32,-0.09,0.38,-0.38,-0.29,-0.56,-0.36,0.03,0.06,-0.04,-0.01,0.19,0.21,0.26,0.24,0.03,0.52,0.5,0.2,0.0,-0.15,0.08,0.14,-0.09,0.23,0.4,0.34,0.29,0.58,0.1,-0.54,-0.34,0.62,0.37,0.36,-0.56,0.93,0.33,0.26,0.04,0.24,0.96,0.28,0.34,0.58,0.86,0.06,-0.17,0.32,0.18,0.12,0.29,-0.14,-1.18,-0.23,-0.47,0.32,0.04,-0.06,0.63,0.3 -0.58,-0.29,-0.45,-0.15,-0.86,-0.36,-0.54,-0.47,-0.29,0.08,-0.58,-0.43,-0.38,-0.36,-0.43,-0.3,-0.32,-0.22,0.08,0.32,0.03,0.16,-0.09,-0.14,0.0,0.08,-0.07,0.11,-0.23,-0.12,-0.01,0.15,0.56,0.46,0.18,0.36,0.42,0.24,0.34,0.42,0.86,0.7,0.15,-0.03,0.19,0.14,0.18,0.03,-0.32,0.69,1.56,1.14,1.15,-0.86,0.74,0.28,0.79,0.96,1.29,0.08,0.44,0.04,0.32,0.46,-0.3,-0.2,-0.51,-0.09,-0.07,2.46,0.23,0.37,-0.15,-0.42,-0.14,-0.64,-0.62,0.69,1.09 -0.36,-0.17,-0.22,-0.34,-0.36,0.03,-0.2,-0.42,-0.15,0.06,-0.2,-0.1,-0.15,-0.4,-0.3,-0.14,-0.64,-0.15,-0.03,0.1,-1.03,-0.23,-0.23,-0.18,-0.17,0.1,-0.03,0.11,0.0,0.07,-0.03,0.26,-0.04,0.75,0.7,0.14,-0.06,-0.2,0.07,0.44,0.37,-0.01,0.15,0.03,-0.51,-0.49,-0.2,-0.23,-0.64,0.11,0.89,0.52,0.87,-0.86,0.57,0.19,-0.27,-0.22,0.39,0.42,0.55,0.46,0.37,-0.06,-0.56,0.07,0.1,0.19,-0.54,0.0,-0.14,-0.14,-0.15,-0.18,0.33,0.16,-0.3,0.49,0.44
%less example.csv
print("%3.2f" % 7)
7.00
print("%3.2f" % 7,end="")
7.00
for i in range(3):
print("%3.2f" % 7,end="")
7.007.007.00
i = "GENE1"
j = "TYR1"
k = ["2","3","4"]
row = [i,j]+k
row
['GENE1', 'TYR1', '2', '3', '4']