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

Jana jahodov... at gmail.com
Sun Mar 17 15:02:56 CET 2013


Dear Ari,
thanks a lot for your response 

this is what I have actually tried before but I got a strange output in my 
logfile (while stderr was empty)
[minos32-1.zcu.cz:06096] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file 
runtime/orte_init.c at line 79
[minos32-1.zcu.cz:06096] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file 
orterun.c at line 694


so I searched thru the documentation for another version of openmpi in 
/software (as I don't have permissions to any other directories of that 
user than bin and lib and yes, he used his own openmpi) and I got 

> [opal_init:startup:internal-failure]
> It looks like opal_init failed for some reason; your parallel process is
> likely to abort.  There are many reasons that a parallel process can
> fail during opal_init; some of which are due to configuration or
> environment problems.  This failure appears to be an internal failure.


So I am confused because from that user's account everything works fine so 
I didn't understand how could this be mpi configuration error.





Dne neděle, 17. března 2013 14:17:07 UTC+1 Ari Paavo Seitsonen napsal(a):
>
> 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 <jahod... at gmail.com <javascript:>>
>
>> 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... at iki.fi <javascript:> / 
> 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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