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

Frank Uhlig uhlig... at gmail.com
Sun Mar 17 14:26:01 CET 2013


Hello Jana,

I agree with Ari (who to my disappointment was faster than me ;-),

export LD_LIBRARY_PATH=/storage/home/$USER/lib:$LD_LIBRARY_PATH

should be the way to go.

Some other things:

Can you tell me what is done with the variable "go" later in the PBS
script? In the lines you provided, you never actually start cp2k.

Furthermore, be careful with your apostrophes. According to the apostrophes
you used in this line:

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

its content will be interpreted in different ways. In this sense the line
is "split" into the following parts:

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

It will still be interpreted as one line by echo, but any part in
apostrophes will be written to $go "as is" (e.g. $LD_LIBRARY_PATH). The
variables will not be substituted by their content. On the other hand,
everything that is not in apostrophes will be substituted in terms of the
contents of the associated variables, e.g., $PATH in the above line will be
substituted by its contents. In general, it is advisable to use quotation
marks for accessing contents of these variables. Depending on how you treat
"$go" that might not matter at all.

It is sufficient to specify -x VARIABLE. You do not need to specify -x
VARIABLE=.... that only makes thing messier.

Btw, it looks like the supercomputer you are referring to is the Czech
metacentrum. If that is correct, then please acknowledge the following. The
version of OpenMPI they use is a reasonable choice (v1.4.3). It is the
prior stable version of OpenMPI and should give no trouble at all.
I am a user at the metacentrum as well and have a working cp2k version
installed with their OpenMPI version and MKL. FFTW3 and libint built
separately and linked statically to the cp2k executable.
Feel free to check out the contents (arch file used was
Linux-x86-64-gfortran.popt) here:

/storage/brno1/home/fuhlig/prog/cp2k-2.3

and a simple, but working test under:

/storage/brno1/home/fuhlig/test_cp2k

Best,

Frank

On Sun, Mar 17, 2013 at 10:45 AM, Jana <jahodov... at gmail.com> wrote:

> 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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