Closed BBR-U22 closed 7 months ago
The provided debug output shows a correct execution.
The issue lies in the environment initialization made by qlogin
. Either:
qlogin
but some variables are withdrawnProvided logs do not help to analyze the issue. To go further, please provide:
qlogin
command and relative environment initializationqlogin
, the output of the module config --dump-state
commandYes, it is something with module initialisation. Oddly that some of the nodes has __MODULES_LMINIT
variable correctly set (but configuration of the nodes is completely identical).
Unfortunately I see no debug options for qlogin (according to man pages and we can not set it globally as it is production system)
LMINIT not set:
$ qlogin node_with_bug
$ env | grep -i modules
MANPATH=/usr/local/Modules/share/man
MODULEPATH_modshare=/share/apps/environmentmodules/centos7/libraries:1:/share/apps/environmentmodules/centos7/general:1:/usr/local/Modules/modulefiles:1:/share/apps/environmentmodules/centos7/devtools:1
MODULES_CMD=/usr/local/Modules/libexec/modulecmd.tcl
ENV=/usr/local/Modules/init/profile.sh
PATH=/usr/local/Modules/bin:/tmp/3109174.1.all.q:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/share/admin/bin:/share/admin/toolsbin
MODULEPATH=/share/apps/environmentmodules/centos7/devtools:/share/apps/environmentmodules/centos7/general:/share/apps/environmentmodules/centos7/libraries:/usr/local/Modules/modulefiles
LOADEDMODULES=
__MODULES_SHARE_MANPATH=:1
BASH_ENV=/usr/local/Modules/init/bash
MODULESHOME=/usr/local/Modules
SGE_O_PATH=/usr/local/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/share/admin/bin:/share/admin/toolsbin
if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then
if [ "$MODULES_REDIRECT_OUTPUT" = '0' ]; then
if [ "$MODULES_REDIRECT_OUTPUT" = '1' ]; then
BASH_FUNC__module_raw()=() { eval "$(/usr/bin/tclsh '/usr/local/Modules/libexec/modulecmd.tcl' bash "$@")";
$ module config --dump-state
Modules Release 5.3.0 (2023-05-14)
- Config. name ---------.- Value (set by if default overridden) ---------------
advanced_version_spec 1
auto_handling 1
avail_indepth 1
avail_output modulepath:alias:dirwsym:sym:tag:variantifspec:key
avail_terse_output modulepath:alias:dirwsym:sym:tag:variantifspec
cache_buffer_bytes 32768
cache_expiry_secs 0
collection_pin_tag 0
collection_pin_version 0
collection_target <undef>
color auto
colors hi=1:db=2:tr=2:se=2:er=91:wa=93:me=95:in=94:mp=1;94:di=94:al=96:va=93:sy=95:de=4:cm=92:aL=100:L=90;47:H=2:F=41:nF=43:S=46:sS=44:kL=30;48;5;109
contact root@localhost
csh_limit 4000
editor vi
extended_default 1
extra_siteconfig <undef>
home /usr/local/Modules (env-var)
icase search
ignore_cache 0
ignore_user_rc 0
ignored_dirs CVS RCS SCCS .svn .git .SYNC .sos
implicit_default 1
implicit_requirement 1
list_output header:idx:variant:sym:tag:key
list_terse_output header
locked_configs
mcookie_check always
mcookie_version_check 1
ml 1
nearly_forbidden_days 14
pager /usr/bin/less -eFKRX
protected_envvars <undef>
quarantine_support 0
rcfile <undef>
redirect_output 1
reset_target_state __init__
run_quarantine <undef>
search_match starts_with
set_shell_startup 0
shells_with_ksh_fpath
silent_shell_debug 0
siteconfig /usr/local/Modules/etc/siteconfig.tcl
tag_abbrev auto-loaded=aL:loaded=L:hidden=H:hidden-loaded=H:forbidden=F:nearly-forbidden=nF:sticky=S:super-sticky=sS:keep-loaded=kL
tag_color_name
tcl_ext_lib /usr/local/Modules/lib/libtclenvmodules.so
tcl_linter nagelfar.tcl
term_background dark
term_width 0
unload_match_order returnlast
variant_shortcut
verbosity normal
wa_277 1
- State name -----------.- Value ----------------------------------------------
WARNING: couldn't find name for group id "20540": Success
always_read_full_file 1
autoinit 0
clock_seconds 1695805955
cmdline /usr/local/Modules/libexec/modulecmd.tcl bash config --dump-state
commandname config
domainname (none)
error_count 0
extra_siteconfig_loaded 0
false_rendered 0
force 0
hiding_threshold 0
inhibit_errreport 0
inhibit_interp 0
init_error_report 1
is_stderr_tty 1
is_win 0
kernelversion #1 SMP Wed Jan 25 16:41:43 UTC 2023
lm_info_cached 0
machine x86_64
modulefile {}
nodename node
os Linux
osversion 3.10.0-1160.83.1.el7.x86_64
paginate 1
path_separator :
report_format regular
reportfd file7
return_false 0
shell bash
shelltype sh
siteconfig_loaded 1
sub1_separator &
sub2_separator |
subcmd config
subcmd_args --dump-state
supported_shells sh bash ksh zsh csh tcsh fish cmd tcl perl python ruby lisp cmake r
tcl_ext_lib_loaded 1
tcl_version 8.5.13
term_columns 213
timer 0
usergroups <undef>
username user
- Env. variable --------.- Value ----------------------------------------------
BASH_FUNC__module_raw() () { eval "$(/usr/bin/tclsh '/usr/local/Modules/libexec/modulecmd.tcl' bash "$@")";
_mlstatus=$?;
return $_mlstatus
}
BASH_FUNC_module() () { local _mlredir=1;
if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then
if [ "$MODULES_REDIRECT_OUTPUT" = '0' ]; then
_mlredir=0;
else
if [ "$MODULES_REDIRECT_OUTPUT" = '1' ]; then
_mlredir=1;
fi;
fi;
fi;
case " $@ " in
*' --no-redirect '*)
_mlredir=0
;;
*' --redirect '*)
_mlredir=1
;;
esac;
if [ $_mlredir -eq 0 ]; then
_module_raw "$@";
else
_module_raw "$@" 2>&1;
fi
}
LOADEDMODULES
MODULEPATH /share/apps/environmentmodules/centos7/devtools:/share/apps/environmentmodules/centos7/general:/share/apps/environmentmodules/centos7/libraries:/usr/local/Modules/modulefiles
MODULEPATH_modshare /share/apps/environmentmodules/centos7/libraries:1:/share/apps/environmentmodules/centos7/general:1:/usr/local/Modules/modulefiles:1:/share/apps/environmentmodules/centos7/devtools:1
MODULESHOME /usr/local/Modules
MODULES_CMD /usr/local/Modules/libexec/modulecmd.tcl
__MODULES_SHARE_MANPATH :1
LMINIT is set:
$ qlogin node_without_bug
$ env | grep -i modules
MANPATH=/usr/local/Modules/share/man
__MODULES_LMINIT=module use --append /share/apps/environmentmodules/centos7/devtools:module use --append /share/apps/environmentmodules/centos7/general:module use --append /share/apps/environmentmodules/centos7/libraries:module use --append /usr/local/Modules/modulefiles
MODULES_CMD=/usr/local/Modules/libexec/modulecmd.tcl
PATH=/usr/local/Modules/bin:/tmp/3109182.1.all.q:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/share/admin/bin:/share/admin/toolsbin
MODULEPATH=/share/apps/environmentmodules/centos7/devtools:/share/apps/environmentmodules/centos7/general:/share/apps/environmentmodules/centos7/libraries:/usr/local/Modules/modulefiles
LOADEDMODULES=
__MODULES_SHARE_MANPATH=:1
MODULESHOME=/usr/local/Modules
SGE_O_PATH=/usr/local/Modules/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/share/admin/bin:/share/admin/toolsbin
if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then
if [ "$MODULES_REDIRECT_OUTPUT" = '0' ]; then
if [ "$MODULES_REDIRECT_OUTPUT" = '1' ]; then
BASH_FUNC__module_raw()=() { eval "$(/usr/bin/tclsh '/usr/local/Modules/libexec/modulecmd.tcl' bash "$@")";
$ module config --dump-state
Modules Release 5.3.0 (2023-05-14)
- Config. name ---------.- Value (set by if default overridden) ---------------
advanced_version_spec 1
auto_handling 1
avail_indepth 1
avail_output modulepath:alias:dirwsym:sym:tag:variantifspec:key
avail_terse_output modulepath:alias:dirwsym:sym:tag:variantifspec
cache_buffer_bytes 32768
cache_expiry_secs 0
collection_pin_tag 0
collection_pin_version 0
collection_target <undef>
color auto
colors hi=1:db=2:tr=2:se=2:er=91:wa=93:me=95:in=94:mp=1;94:di=94:al=96:va=93:sy=95:de=4:cm=92:aL=100:L=90;47:H=2:F=41:nF=43:S=46:sS=44:kL=30;48;5;109
contact root@localhost
csh_limit 4000
editor vi
extended_default 1
extra_siteconfig <undef>
home /usr/local/Modules (env-var)
icase search
ignore_cache 0
ignore_user_rc 0
ignored_dirs CVS RCS SCCS .svn .git .SYNC .sos
implicit_default 1
implicit_requirement 1
list_output header:idx:variant:sym:tag:key
list_terse_output header
locked_configs
mcookie_check always
mcookie_version_check 1
ml 1
nearly_forbidden_days 14
pager /usr/bin/less -eFKRX
protected_envvars <undef>
quarantine_support 0
rcfile <undef>
redirect_output 1
reset_target_state __init__
run_quarantine <undef>
search_match starts_with
set_shell_startup 0
shells_with_ksh_fpath
silent_shell_debug 0
siteconfig /usr/local/Modules/etc/siteconfig.tcl
tag_abbrev auto-loaded=aL:loaded=L:hidden=H:hidden-loaded=H:forbidden=F:nearly-forbidden=nF:sticky=S:super-sticky=sS:keep-loaded=kL
tag_color_name
tcl_ext_lib /usr/local/Modules/lib/libtclenvmodules.so
tcl_linter nagelfar.tcl
term_background dark
term_width 0
unload_match_order returnlast
variant_shortcut
verbosity normal
wa_277 1
- State name -----------.- Value ----------------------------------------------
WARNING: couldn't find name for group id "20497": Success
always_read_full_file 1
autoinit 0
clock_seconds 1695806887
cmdline /usr/local/Modules/libexec/modulecmd.tcl bash config --dump-state
commandname config
domainname (none)
error_count 0
extra_siteconfig_loaded 0
false_rendered 0
force 0
hiding_threshold 0
inhibit_errreport 0
inhibit_interp 0
init_error_report 1
is_stderr_tty 1
is_win 0
kernelversion #1 SMP Wed Jan 25 16:41:43 UTC 2023
lm_info_cached 0
machine x86_64
modulefile {}
nodename node
os Linux
osversion 3.10.0-1160.83.1.el7.x86_64
paginate 1
path_separator :
report_format regular
reportfd file7
return_false 0
shell bash
shelltype sh
siteconfig_loaded 1
sub1_separator &
sub2_separator |
subcmd config
subcmd_args --dump-state
supported_shells sh bash ksh zsh csh tcsh fish cmd tcl perl python ruby lisp cmake r
tcl_ext_lib_loaded 1
tcl_version 8.5.13
term_columns 213
timer 0
usergroups <undef>
username user
- Env. variable --------.- Value ----------------------------------------------
BASH_FUNC__module_raw() () { eval "$(/usr/bin/tclsh '/usr/local/Modules/libexec/modulecmd.tcl' bash "$@")";
_mlstatus=$?;
return $_mlstatus
}
BASH_FUNC_module() () { local _mlredir=1;
if [ -n "${MODULES_REDIRECT_OUTPUT+x}" ]; then
if [ "$MODULES_REDIRECT_OUTPUT" = '0' ]; then
_mlredir=0;
else
if [ "$MODULES_REDIRECT_OUTPUT" = '1' ]; then
_mlredir=1;
fi;
fi;
fi;
case " $@ " in
*' --no-redirect '*)
_mlredir=0
;;
*' --redirect '*)
_mlredir=1
;;
esac;
if [ $_mlredir -eq 0 ]; then
_module_raw "$@";
else
_module_raw "$@" 2>&1;
fi
}
LOADEDMODULES
MODULEPATH /share/apps/environmentmodules/centos7/devtools:/share/apps/environmentmodules/centos7/general:/share/apps/environmentmodules/centos7/libraries:/usr/local/Modules/modulefiles
MODULESHOME /usr/local/Modules
MODULES_CMD /usr/local/Modules/libexec/modulecmd.tcl
__MODULES_LMINIT module use --append /share/apps/environmentmodules/centos7/devtools:module use --append /share/apps/environmentmodules/centos7/general:module use --append /share/apps/environmentmodules/centos7/libraries:module use --append /usr/local/Modules/modulefiles
__MODULES_SHARE_MANPATH :1
Thanks for these inputs.
node_with_bug is configured differently than node_without_bug. ENV
and BASH_ENV
variables are defined on node_with_bug. Which means set_shell_startup
option is enabled on this node, whereas it is disabled on node_without_bug.
There is another awkward difference that I spot: MODULEPATH_modshare
is defined on node_with_bug but such variable is only defined on Modules v4 (not v5).
So I would suggest to check the differences between node_with_bug and node_without_bug filesystems:
Describe the bug
Modules Release 5.3.0 (2023-05-14)
In UGE jobsMODULEPATH
variable is cleared withmodule stash
command and set back onmodule stashpop
(__MODULES_LMINIT
is not set in jobs). It is fine when ssh though.To Reproduce
Location and content of any modulerc or modulefile involved:
Expected behavior
List of modules after
module statsh
Error and debugging information
Additional context