Re: [Condor-users] libreadline.so.5: cannot open shared object file

[Todd Tannenbaum <tannenba@xxxxxxxxxxx>]

ychung@xxxxxxxxxxx wrote:
> Hello,
>
> I tried to submit files on /scratch of bigmem02 (in statistic department),
> but I got this error:
>
>  /scratch/condor/execute/dir_3140/condor_exec.exe: error while loading
> shared libraries: libreadline.so.5: cannot open shared object file: No
> such
> file or directory

Hi Yujin -

Todd here w/ the UW Condor Project.

Couple items - condor-users@xxxxxxxxxxx is a general-purpose best effort 
forum where Condor users can help each other out... as you are a UW 
researcher asking questions that are specific to the computing 
environment at UW, you may instead prefer to send questions to 
condor-admin@xxxxxxxxxxxx

But onto the real business of trying to help you w/ the issue 
above/below:  I don't think the problem has anything to do with where 
you submitted your job.  Instead, it looks to me that the problem is the 
Computer Sciences Lab (CSL), the group that maintains all the machines 
in the UW CS and Stats dept, does not have a consistent set of packages 
installed across all of the 64bit red hat boxes they manager.  If your 
job happens to land on a machine that has file
  /usr/lib/libreadline.so.5
installed, all is good.  If your job happens to run on a machine like 
ale-22.cs.wisc.edu where this file is inexplicably missing, the result 
is the error message you reported above.

I will open a ticket w/ the CSL asking them to install this library on 
all stats/cs machines (and cc you).

In the meantime, you could workaround this problem several different ways:

One possibility, if you have the source code to the program you are 
trying to run, is to compile it statically so it does not rely on the 
presence of this file in /usr/lib --- just add /usr/lib/libreadline.a to 
the list of files you are passing to your compiler or linker (e.g. gcc 
or whatever).

Another possibility would be to ask Condor to move libreadline.so.5 
along with your job, and then set the environment variable 
LD_LIBRARY_PATH to use it.  So use a Condor submit file that looks like 
this (note: i didn't test this, I just edited your submit example below):
 Executable   = /afs/cs.wisc.edu/u/y/c/ychung/bin/mbbest2.2
 Universe     = vanilla
 input = mbBest.nex
 output = mbBest.log
 Log  = condor.log
 error = condor.error
 Requirements  = Memory >= 64 && OpSys == "LINUX"
 should_transfer_files = YES
 when_to_transfer_output = ON_EXIT_OR_EVICT
 transfer_input_files = /usr/lib/libreadline.so.5, mbBest.nex, 
sequence_16.nex
 Environment = "LD_LIBRARY_PATH=""."""
 Queue

hope the above helps,
Todd


> and log:
>
> 000 (014.000.000) 05/18 13:28:01 Job submitted from host:
> <128.105.109.52:34266>
> ...
> 001 (014.000.000) 05/18 13:30:07 Job executing on host:
> <128.105.150.122:53999>
> ...
> 005 (014.000.000) 05/18 13:30:09 Job terminated.
>         (1) Normal termination (return value 127)
>                 Usr 0 00:00:00, Sys 0 00:00:00  -  Run Remote Usage
>                 Usr 0 00:00:00, Sys 0 00:00:00  -  Run Local Usage
>                 Usr 0 00:00:00, Sys 0 00:00:00  -  Total Remote Usage
>                 Usr 0 00:00:00, Sys 0 00:00:00  -  Total Local Usage
>         164  -  Run Bytes Sent By Job
>         1386270  -  Run Bytes Received By Job
>         164  -  Total Bytes Sent By Job
>         1386270  -  Total Bytes Received By Job
>
>
>
> The same thing happened when I tried it on bigmem01 and desk21.
>
>
> Here is my submit file:
>
>   Executable   = /afs/cs.wisc.edu/u/y/c/ychung/bin/mbbest2.2
>   Universe     = vanilla
>  input = mbBest.nex
>   output = mbBest.log
>     Log  = condor.log
> error = condor.error
>   Requirements  = Memory >= 64 && OpSys == "LINUX"
> should_transfer_files = YES
> when_to_transfer_output = ON_EXIT_OR_EVICT
>  transfer_input_files = mbBest.nex, sequence_16.nex
> Queue
>
>
> It worked well on AFS with this submit file:
>   Executable   = mbbest2.2
>   Universe     = vanilla
>   input = mbBest.nex
> output = logOut
>   Requirements  = Memory >= 64 && OpSys == "LINUX"
>     Log          = foo.log
>   Queue
>
>
> Where is the problem? Do you think bigmem01-02 and desk21 are not
> available for using condor? Is there any wrong on my submit file?
>
> Thank you in advance!
>
>
> Best regards,
> Yujin
>
>
>
>
>
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