Dear Ari,<div>thanks a lot for your response </div><div><br></div><div>this is what I have actually tried before but I got a strange output in my logfile (while stderr was empty)</div><div><div>[minos32-1.zcu.cz:06096] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file runtime/orte_init.c at line 79</div><div>[minos32-1.zcu.cz:06096] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file orterun.c at line 694</div><div><br></div><div><br></div><div>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 </div><div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex;">[opal_init:startup:internal-failure]<br>It looks like opal_init failed for some reason; your parallel process is<br>likely to abort. There are many reasons that a parallel process can<br>fail during opal_init; some of which are due to configuration or<br>environment problems. This failure appears to be an internal failure.</blockquote></div><div><br></div><div>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.</div><div><br></div><div><br></div><div><br></div><div><br></div><br>Dne neděle, 17. března 2013 14:17:07 UTC+1 Ari Paavo Seitsonen napsal(a):<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Dear Jana(?),<div><br></div><div> I don't know whether this helps, but a few notes:</div><div><br></div><div> - With the second "export LD_LIBRARY_PATH..." you overwrite the first assigment; is this what you wanted? Usually one uses</div>
<div>export LD_LIBRARY_PATH=${LD_LIBRARY_<wbr>PATH}:<new_directory> (or prepending the <new_directory>)</div><div><br></div><div> - The value of the second assignment points to a dynamic library directly, but it should point to a _directory_</div>
<div><br></div><div> - 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</div>
<div><br></div><div> Greetings,</div><div><br></div><div> apsi</div></div><div><br><br><div class="gmail_quote">2013/3/17 Jana <span dir="ltr"><<a href="javascript:" target="_blank" gdf-obfuscated-mailto="vzPZnxtfHwkJ">jahod...@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all, <div>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.</div>
<div><br></div><div>I got his binary and dynamically linked libs via cp -a so with links, but I keep getting</div><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
$ ldd ./bin/mpiexec<br> linux-vdso.so.1 => (0x00007fff12a74000)<br> libopen-rte.so.4 => not found</blockquote></div><div>or </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
$ ldd /storage/home/his-username/<wbr>bin/mpiexec<br> linux-vdso.so.1 => (0x00007fff2cdff000)<br> libopen-rte.so.4 => not found</blockquote><div><br></div><div>while he has at the same time</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<span style="font-family:arial,sans-serif">$ ldd /home/his-username/storage/<wbr>bin/</span><u></u><span style="font-family:arial,sans-serif">mpiexec<br></span><span style="font-family:arial,sans-serif"> linux-vdso.so.1 => (0x00007fff57d33000)<br>
</span><span style="font-family:arial,sans-serif"> libopen-rte.so.4 => /home/his-username/CP2K/lib/<wbr>libopen-</span><u></u><span style="font-family:arial,sans-serif">rte.so.4 (0x00007fdb28ffd000)</span></blockquote>
<div><br></div><div>I changed my script for PBS so that I added the red line<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
...<br>echo 'export LD_LIBRARY_PATH=/storage/home/<wbr>$USER/lib' >> $go<br>echo 'export PATH=/storage/home/$USER/bin:'<wbr>$PATH >> $go<br>echo 'echo "env:"; env' >> $go<br>echo 'echo "nodes:"; cat $PBS_NODEFILE; echo libs:; ls /storage/home/$USER/lib; echo bin:; ls /storage/home/$USER/bin' >> $go<br>
<font color="#cc0000">echo 'export LD_LIBRARY_PATH=/storage/home/<wbr>$USER/lib/libopen-rte.so.4' >> $go<br></font>echo /storage/home/$USER/bin/'<wbr>mpiexec --hostfile $PBS_NODEFILE -x LD_LIBRARY_PATH='$LD_LIBRARY_<wbr>PATH' -x PATH='$PATH' cp2k.popt '$base'.in > '$base'.log 2>&1' >> $go<br>
...</blockquote><div><br></div><div>but in the logfile (using input for h2o from regtests) I keep getting</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
/storage/home/mathausj/bin/<wbr>mpiexec: error while loading shared libraries: libopen-rte.so.4: cannot open shared object file: No such file or directory</blockquote><div><br></div><div><br></div><div>though</div><div><br></div>
<div><br></div><div><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small">$ ls lib</div><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small">total 15936</div><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small">
-rwxr-xr-x 1 mathausj meta 20323 2013-03-14 09:59 libmpi_f90.so.3</div><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small">-rwxr-xr-x 1 mathausj meta 2002819 2013-03-14 09:59 libmpi_f77.so.1</div>
<div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small">-rwxr-xr-x 1 mathausj meta 10282011 2013-03-14 09:59 libmpi.so.1</div><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small">
-rwxr-xr-x 1 mathausj meta 4006084 2013-03-14 16:52 libopen-rte.so.4</div><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small"><br></div><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small">
<br></div><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small">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...</div>
<span><font color="#888888"><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small"><br></div><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small"><br></div>
</font></span></div><span><font color="#888888">
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=<wbr>*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=<wbr>-=*=-=*=-=*=-=*=-<br> Ari P Seitsonen / <a href="javascript:" target="_blank" gdf-obfuscated-mailto="vzPZnxtfHwkJ">Ari.P...@iki.fi</a> / <a href="http://www.iki.fi/~apsi/" target="_blank">http://www.iki.fi/~apsi/</a><br>
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