Hello Jana,<br><br>I agree with Ari (who to my disappointment was faster than me ;-), <br><br><font color="#cc0000">export LD_LIBRARY_PATH=/storage/home/$USER/lib:$LD_LIBRARY_PATH <br><br><font color="#000000">should be the way to go.<br>
</font></font><br>Some other things:<br><br>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. <br>
<br>Furthermore, be careful with your apostrophes. According to the apostrophes you used in this line:<br><br>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' >> $go<br>
<br>its content will be interpreted in different ways. In this sense the line is "split" into the following parts:<br>
<br>echo <br>/storage/home/$USER/bin/<br>'mpiexec --hostfile $PBS_NODEFILE -x LD_LIBRARY_PATH='<br>$LD_LIBRARY_PATH<br>' -x PATH='<br>$PATH<br>' cp2k.popt '<br>$base<br>'.in > '<br>$base<br>
'.log 2>&1'<br> >> $go<br><br>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.<br>
<br>It is sufficient to specify -x VARIABLE. You do not need to specify -x VARIABLE=.... that only makes thing messier. <br><br>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. <br>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.<br>
Feel free to check out the contents (arch file used was Linux-x86-64-gfortran.popt) here:<br><br>/storage/brno1/home/fuhlig/prog/cp2k-2.3<br><br>and a simple, but working test under:<br><br>/storage/brno1/home/fuhlig/test_cp2k<br>
<br>Best,<br><br>Frank<br><br><div class="gmail_quote">On Sun, Mar 17, 2013 at 10:45 AM, Jana <span dir="ltr"><<a href="mailto:jahodov...@gmail.com" target="_blank">jahodov...@gmail.com</a>></span> wrote:<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/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/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/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/$USER/lib' >> $go<br>echo 'export PATH=/storage/home/$USER/bin:'$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' >> $go<br>
<font color="#cc0000">echo 'export LD_LIBRARY_PATH=/storage/home/$USER/lib/libopen-rte.so.4' >> $go<br></font>echo /storage/home/$USER/bin/'mpiexec --hostfile $PBS_NODEFILE -x LD_LIBRARY_PATH='$LD_LIBRARY_PATH' -x PATH='$PATH' cp2k.popt '$base'.in > '$base'.log 2>&1' >> $go<br>
...</blockquote><div><br></div><div>but in the logfile (using input for h2o from regtests) I keep getting</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
/storage/home/mathausj/bin/mpiexec: error while loading shared libraries: libopen-rte.so.4: cannot open shared object file: No such file or directory</blockquote><div><br></div><div><br></div><div>though</div><div><br></div>
<div><br></div><div><div style="color:rgb(51,51,51);font-family:verdana,sans-serif;font-size:small">$ 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">
<p></p>
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