Module avail throws libuuid.so.1: no version information available (required by /lib64/libblkid.so.1) error

himanshisyadav commented 2 years ago

When I run module avail I get the following error message:

ERROR: logger: /software/python-anaconda-2022.05-el8-x86_64/lib/libuuid.so.1: no version information available (required by /lib64/libblkid.so.1)
      while executing
  "exec logger -t modulecmd "[get-env USER]: $command [join $args]""
      (procedure "module" line 2)
      invoked from within
  "module avail"
      ("eval" body line 1)
      invoked from within
  "eval $execcmdlist"
  Please report this issue at https://github.com/cea-hpc/modules/issues

Output of:

conda package -w /software/python-anaconda-2022.05-el8-x86_64/lib/libuuid.so.1

is:

/software/python-anaconda-2022.05-el8-x86_64/lib/libuuid.so.1 defaults/linux-64::libuuid-1.0.3-h7f8727e_2

xdelaruelle commented 2 years ago

Thanks for your report.

The module installation you use is configured to log each command call with the logger tool. This is done with a siteconfig.tcl configuration file similar to the one described in the log module command.

The logger command seems relying on the libuuid.so.1 library on your system. I assume that the python-anaconda you enable in your environment adds its library directory into LD_LIBRARY_PATH environment variable. As this directory contains a version of libuuid.so.1, logger tries to use this library version but it is not compatible, thus it leads to the error you obtain.

I can reproduce a similar issue on my side:

$ ldd /usr/bin/logger
    linux-vdso.so.1 (0x00007ffe207f9000)
    libsystemd.so.0 => /lib64/libsystemd.so.0 (0x00007f61c0065000)
    libc.so.6 => /lib64/libc.so.6 (0x00007f61bfe00000)
    liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f61c003a000)
    libzstd.so.1 => /lib64/libzstd.so.1 (0x00007f61bfd4d000)
    liblz4.so.1 => /lib64/liblz4.so.1 (0x00007f61c0016000)
    libcap.so.2 => /lib64/libcap.so.2 (0x00007f61c000c000)
    libgcrypt.so.20 => /lib64/libgcrypt.so.20 (0x00007f61bfc10000)
    libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f61bfbf0000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f61c016f000)
    libgpg-error.so.0 => /lib64/libgpg-error.so.0 (0x00007f61bfbca000)
$ mkdir tmp
$ touch tmp/libgpg-error.so.0
$ export LD_LIBRARY_PATH=$(pwd)/tmp
$ module avail
...
ERROR: logger: error while loading shared libraries: /path/to/dir/tmp/libgpg-error.so.0: file too short
      while executing
  "exec logger -t module "{ \"user\": \"[get-env USER]\", \"cmd\": \"$cmdname\", \"args\": \"$args\" }""
      (procedure "logModuleCmd" line 14)
      invoked from within
  "logModuleCmd {module av} 0 {} leave"
      (leave trace on "{*}$execcmdlist")
  Please report this issue at https://github.com/cea-hpc/modules/issues

To solve such issue, logger should be run without being affected by library directories defined in LD_LIBRARY_PATH environment variable.

One way to do that is to unset this environment variable prior executing logger:

set ORIG_LD_LIBRARY_PATH $::env(ORIG_LD_LIBRARY_PATH)
exec logger -t modulecmd "[get-env USER]: $command [join $args]" 
set ::env(ORIG_LD_LIBRARY_PATH) $ORIG_LD_LIBRARY_PATH

I will update the log module command cookbook recipe to take this situation into account.

himanshisyadav commented 1 year ago

Thank you for your solution!

Unfortunately, that didn't work and I don't know how exactly I should proceed from here.

xdelaruelle commented 1 year ago

Could you please provide me the siteconfig.tcl file used on your side.

Could you also provide the output of a module config --dump-state command.

himanshisyadav commented 1 year ago

Sure!

Here are the contents of siteconfig.tcl file:


# SITECONFIG.TCL, site-specific configuration script for Modules
#
# This Tcl script enables to supersede any global variable or procedure
# definition of modulecmd.tcl. See 'Modulecmd startup' section in module(1)
# manpage for detailed information.

##########################################################################

# uncomment the following line to forbid the definition of an extra
# site-specific configuration script
#lappendConf locked_configs extra_siteconfig

# uncomment the following line to forbid `implicit_default` config option
# superseding
#lappendConf locked_configs implicit_default

# SITECONFIG.TCL, site-specific configuration script for Modules
#
# This Tcl script enables to supersede any global variable or procedure
# definition of modulecmd.tcl. See 'Modulecmd startup' section in module(1)
# manpage for detailed information.

##########################################################################

# uncomment the following line to forbid the definition of an extra
# site-specific configuration script
#lappendConf locked_configs extra_siteconfig

# uncomment the following line to forbid `implicit_default` config option
# superseding
#lappendConf locked_configs implicit_default

rename ::module ::__module
proc module {command args} {
   exec logger -t modulecmd "[get-env USER]: $command [join $args]"
   return [eval __module "{$command}" $args]
}
rename ::module ::__module
proc module {command args} {
   exec logger -t modulecmd "[get-env USER]: $command [join $args]"
   return [eval __module "{$command}" $args]
}

Output of the module config --dump-state is

Modules Release 4.6.1+XX-g8159ac3d (2020-12-15)

- Config. name ---------.- Value (set by if default overridden) ---------------
advanced_version_spec     0
auto_handling             0
avail_indepth             1
avail_report_dir_sym      1
avail_report_mfile_sym    1
collection_pin_version    0
collection_target         <undef>
color                     never
colors                    hi=1:db=2:tr=2:se=2:er=91:wa=93:me=95:in=94:mp=1;94:di=94:al=96:sy=95:de=4:cm=92
contact                   root@localhost
csh_limit                 4000
extended_default          0
extra_siteconfig          <undef>
home                      /software/modules (env-var)
icase                     never
ignored_dirs              CVS RCS SCCS .svn .git .SYNC .sos
implicit_default          1
implicit_requirement      1
locked_configs            
ml                        1
nearly_forbidden_days     14
pager                     /usr/bin/less -eFKRX
rcfile                    <undef>
run_quarantine            <undef>
search_match              starts_with
set_shell_startup         1
shells_with_ksh_fpath     
silent_shell_debug        <undef>
siteconfig                /software/modules/etc/siteconfig.tcl
tcl_ext_lib               /software/modules/lib/libtclenvmodules.so
term_background           dark
unload_match_order        returnlast
verbosity                 concise (env-var)
wa_277                    0

- State name -----------.- Value ----------------------------------------------
autoinit                  0
clock_seconds             1664909057
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 Sep 15 15:39:39 UTC 2021
lm_info_cached            0
:

Thank you!

xdelaruelle commented 1 year ago

Now that I read again the code I proposed, I see that it is totally wrong. Sorry for that. The correct fix code should be:

   if {[info exists ::env(LD_LIBRARY_PATH)]} {
      set ORIG_LD_LIBRARY_PATH $::env(LD_LIBRARY_PATH)
      unset ::env(LD_LIBRARY_PATH)
   }
   exec logger -t modulecmd "[get-env USER]: $command [join $args]"
   if {[info exists ORIG_LD_LIBRARY_PATH]} {
      set ::env(LD_LIBRARY_PATH) $ORIG_LD_LIBRARY_PATH
   }

So I suggest you update the siteconfig.tcl file on your side to look like:

# SITECONFIG.TCL, site-specific configuration script for Modules
#
# This Tcl script enables to supersede any global variable or procedure
# definition of modulecmd.tcl. See 'Modulecmd startup' section in module(1)
# manpage for detailed information.

##########################################################################

# uncomment the following line to forbid the definition of an extra
# site-specific configuration script
#lappendConf locked_configs extra_siteconfig

# uncomment the following line to forbid `implicit_default` config option
# superseding
#lappendConf locked_configs implicit_default

rename ::module ::__module
proc module {command args} {
   if {[info exists ::env(LD_LIBRARY_PATH)]} {
      set ORIG_LD_LIBRARY_PATH $::env(LD_LIBRARY_PATH)
      unset ::env(LD_LIBRARY_PATH)
   }
   exec logger -t modulecmd "[get-env USER]: $command [join $args]"
   if {[info exists ORIG_LD_LIBRARY_PATH]} {
      set ::env(LD_LIBRARY_PATH) $ORIG_LD_LIBRARY_PATH
   }
   return [eval __module "{$command}" $args]
}

cea-hpc / modules

Module avail throws libuuid.so.1: no version information available (required by /lib64/libblkid.so.1) error #475