[CP2K:4336] Trouble with libopen-rte.so.4

Ari Paavo Seitsonen ari.p.s... at gmail.com
Sun Mar 17 14:17:07 CET 2013


Dear Jana(?),

  I don't know whether this helps, but a few notes:

 - With the second "export LD_LIBRARY_PATH..." you overwrite the first
assigment; is this what you wanted? Usually one uses
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:<new_directory> (or prepending
the <new_directory>)

 - The value of the second assignment points to a dynamic library directly,
but it should point to a _directory_

 - This problem comes directly from the 'mpiexec', not CP2K itself. It
seems that the user has compiled the MPI oneself; hopefully this is useful
on your machine: In general it is the system administrators who set up a
consistent and working MPI environment

    Greetings,

       apsi


2013/3/17 Jana <jahodov... at gmail.com>

> Dear all,
> I have managed to compile cp2k-2.3 at a supercomputer using their mklroot,
> mpi and my fftw and libint but there is a problem with run while using
> different nodes probably due to the old version of mpi available...so i was
> sent another version compiled by another user at the same supercomputer but
> the user didn't use anything default, all libs his own.
>
> I got his binary and dynamically linked libs via cp -a so with links, but
> I keep getting
>
>> $ ldd ./bin/mpiexec
>>         linux-vdso.so.1 =>  (0x00007fff12a74000)
>>         libopen-rte.so.4 => not found
>
> or
>
>> $ ldd /storage/home/his-username/bin/mpiexec
>>         linux-vdso.so.1 =>  (0x00007fff2cdff000)
>>         libopen-rte.so.4 => not found
>
>
> while he has at the same time
>
>> $ ldd /home/his-username/storage/bin/**mpiexec
>>         linux-vdso.so.1 =>  (0x00007fff57d33000)
>>         libopen-rte.so.4 => /home/his-username/CP2K/lib/libopen-**rte.so.4
>> (0x00007fdb28ffd000)
>
>
> I changed my script for PBS so that I added the red line
>
>> ...
>> echo 'export LD_LIBRARY_PATH=/storage/home/$USER/lib' >> $go
>> echo 'export PATH=/storage/home/$USER/bin:'$PATH >> $go
>> echo 'echo "env:"; env' >> $go
>> echo 'echo "nodes:"; cat $PBS_NODEFILE; echo libs:; ls
>> /storage/home/$USER/lib; echo bin:; ls /storage/home/$USER/bin' >> $go
>> echo 'export LD_LIBRARY_PATH=/storage/home/$USER/lib/libopen-rte.so.4' >>
>> $go
>> echo /storage/home/$USER/bin/'mpiexec --hostfile $PBS_NODEFILE -x
>> LD_LIBRARY_PATH='$LD_LIBRARY_PATH' -x PATH='$PATH' cp2k.popt '$base'.in >
>> '$base'.log 2>&1' >> $go
>> ...
>
>
> but in the logfile (using input for h2o from regtests) I keep getting
>
>> /storage/home/mathausj/bin/mpiexec: error while loading shared libraries:
>> libopen-rte.so.4: cannot open shared object file: No such file or directory
>
>
>
> though
>
>
> $ ls lib
> total 15936
> -rwxr-xr-x 1 mathausj meta    20323 2013-03-14 09:59 libmpi_f90.so.3
> -rwxr-xr-x 1 mathausj meta  2002819 2013-03-14 09:59 libmpi_f77.so.1
> -rwxr-xr-x 1 mathausj meta 10282011 2013-03-14 09:59 libmpi.so.1
> -rwxr-xr-x 1 mathausj meta  4006084 2013-03-14 16:52 libopen-rte.so.4
>
>
> I am sorry to bother you with this problem, but I am really clueless...
> Have emailed helpdesk and the user who compiled it but none of them has
> solution to this problem, if executed from that user's account, cp2k works
> perfectly...
>
>
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>



-- 
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
  Ari P Seitsonen / Ari.P.S... at iki.fi / http://www.iki.fi/~apsi/
  Physikalisch-Chemisches Institut der Universität Zürich
  Tel: +41 44 63 55 44 97  /  Mobile: +41 79 71 90 935
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