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<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">Dear users,<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">since the operating system of the cluster I am running my application on with PETSC (Version 3.19) has been changed
from CentOS 7 to Rocky Linux 8 and also the module system has been changed to Lmod, I get the following error message when running my application: <o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">Primary job terminated normally, but 1 process returned</span></i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">a non-zero exit code. Per user-direction, the job has been aborted.</span></i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">mpiexec noticed that process rank 0 with PID 0 on node login18-x-2 exited on signal 15 (Terminated).</span></i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">make: *** [Makefile:96: cathode-run] Error 143</span></i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">When running the application with <i>LD_DEBUG=files</i>, it says that certain symbols cannot be looked up by PETSC,
e.g.:<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white;vertical-align:baseline"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">/cvmfs/software.hpc.rwth.de/Linux/RH8/x86_64/intel/skylake_avx512/software/UCX/1.12.1-GCCcore-11.3.0/lib/ucx/libuct_cma.so.0:
error: symbol lookup error: undefined symbol: ucs_module_global_init (fatal)<o:p></o:p></span></i></p>
<p class="MsoNormal" style="background:white;vertical-align:baseline"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">[…]<o:p></o:p></span></i></p>
<p class="MsoNormal" style="background:white;vertical-align:baseline"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">/rwthfs/rz/cluster/home/mh787286/petsc/arch-linux-c-debug/lib/libpetsc.so.3.19: error:
symbol lookup error: undefined symbol: MPID_Abort (fatal)<o:p></o:p></span></i></p>
<p class="MsoNormal" style="background:white;vertical-align:baseline"><i><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">/rwthfs/rz/cluster/home/mh787286/petsc/arch-linux-c-debug/lib/libpetsc.so.3.19: error:
symbol lookup error: undefined symbol: ps_tool_initialize (fatal)<o:p></o:p></span></i></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">I attached the output in the "LD_DEBUG_make_cathode-run" file. When I look up the dependencies of libpetsc.so.3.19
with the <i>ldd</i> command, I can find the locations of the dependent libraries listed in the LD_LIBRARY_PATH (see configure.log). Thus, PETSC should be able to link to these libraries.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">I load the modules GCC/11.3.0 and OpenMPI/4.1.4. Furthermore, please also find the make file attached as "Makefile"
as well as the configure.log and make.log.<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">Is there anything I need to change in the make file to adapt it to the new module system, or are there any issues
with missing links/ libraries after the update?<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span lang="EN-US" style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE">Matthias<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;color:black;mso-ligatures:none;mso-fareast-language:DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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