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<p>Dear professor:</p>
<p><br>
</p>
<p>I use Open MPI, version 1.4.5.</p>
<p><br>
</p>
<p>I added "-C -g" because some people in the mail-list said it probably will solve the problem. </p>
<p>Thanks for your advice, I will recompile the package soon. </p>
<br>
Sincerely
<div>Wangwei<br>
<div style="color: rgb(0, 0, 0);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> wien-bounces@zeus.theochem.tuwien.ac.at <wien-bounces@zeus.theochem.tuwien.ac.at> on behalf of Laurence Marks <L-marks@northwestern.edu><br>
<b>Sent:</b> Tuesday, July 28, 2015 15:36<br>
<b>To:</b> A Mailing list for WIEN2k users<br>
<b>Subject:</b> Re: [Wien] Segmentation fault in Supercell Calculation</font>
<div> </div>
</div>
<div>
<div dir="ltr">N.B., unless you are a code developer "-C -g" are a terrible idea. Remove them, they may easily lead to the code crashing. Replace them by just "-O1"</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jul 28, 2015 at 3:28 PM, Lan, Wangwei <span dir="ltr">
<<a href="mailto:wl13c@my.fsu.edu" target="_blank" title="mailto:wl13c@my.fsu.edu
Ctrl+Click or tap to follow the link">wl13c@my.fsu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Dear Professor:</p>
<p><br>
</p>
<p><br>
</p>
<p>When I type "mpif90 --version", it give me " ifort (IFORT) 12.1.3 20120212". So, I thought it should work.</p>
<p><br>
</p>
<p>My Libraries linking are listed below:</p>
<p>Parallel excution:</p>
<div> </div>
<div> FFTW_LIB + FFTW_OPT : -lfftw3_mpi -lfftw3 -L/opt/fftw3.3.3/lib + -DFFTW3 -I/opt/fftw3.3.3/include (already set)</div>
<div> RP RP_LIB(SCALAPACK+PBLAS): -lmkl_scalapack_lp64 -lmkl_blacs_lp64 $(R_LIBS) </div>
<div> FP FPOPT(par.comp.options): -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io</div>
<div> </div>
<div>Compiler Option</div>
<br>
<div> O Compiler options: -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io -C -g</div>
<div> F FFTW options: -DFFTW3 -I/opt/fftw3.3.3/include</div>
<div> L Linker Flags: $(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread</div>
<div> P Preprocessor flags '-DParallel'</div>
<div> R R_LIB (LAPACK+BLAS): -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lmkl_solver_lp64</div>
<div> FL FFTW_LIBS: -lfftw3_mpi -lfftw3 -L/opt/fftw3.3.3/lib</div>
<div style="color:rgb(0,0,0)"><br>
</div>
<div style="color:rgb(0,0,0)"><br>
</div>
<div style="color:rgb(0,0,0)"><br>
</div>
<div style="color:rgb(0,0,0)">Sincerely</div>
<div style="color:rgb(0,0,0)">Wangwei </div>
<div style="color:rgb(0,0,0)"><br>
<hr style="display:inline-block; width:98%">
<div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b>
<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a> <<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a>> on behalf of Laurence
Marks <<a href="mailto:L-marks@northwestern.edu" target="_blank">L-marks@northwestern.edu</a>><br>
<b>Sent:</b> Tuesday, July 28, 2015 14:59<br>
<b>To:</b> A Mailing list for WIEN2k users<br>
<b>Subject:</b> Re: [Wien] Segmentation fault in Supercell Calculation</font>
<div> </div>
</div>
<div>
<div dir="ltr">Your options are probably wrong:
<div><br>
</div>
<div>a) mpif90 is normally gfortran, the Intel version is mpiifort</div>
<div>b) It is easy to use the wrong linking with the Intel mkl libraries. Please provide the information I requested.</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jul 28, 2015 at 2:55 PM, Lan, Wangwei <span dir="ltr">
<<a href="mailto:wl13c@my.fsu.edu" target="_blank">wl13c@my.fsu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<p><span style="font-size:12pt">Dear Professor:</span></p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">Yes, "x lapw0" works without mpi.</span><br>
</p>
<p><span style="font-size:12pt"><br>
</span></p>
<p>My mpi compile : mpif90</p>
<p>I use Open MPI， version 1.4.5</p>
<p>the parallel compilation options are </p>
<div><br>
</div>
-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback -assume buffered_io<br>
<br>
I use Intel MKL libraries, that part should be fine.
<div><br>
</div>
<div><br>
</div>
<div>Thanks very much for your help.</div>
<div><br>
</div>
<div>Sincerely </div>
<div>Wangwei Lan</div>
<div>
<div style="color:rgb(0,0,0)">
<hr style="display:inline-block; width:98%">
<div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b>
<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a> <<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a>> on behalf of Laurence
Marks <<a href="mailto:L-marks@northwestern.edu" target="_blank">L-marks@northwestern.edu</a>><br>
<b>Sent:</b> Tuesday, July 28, 2015 14:30<br>
<b>To:</b> A Mailing list for WIEN2k users<br>
<b>Subject:</b> Re: [Wien] Segmentation fault in Supercell Calculation</font>
<div> </div>
</div>
<div>
<div dir="ltr">Does a simple "x lapw0" work, i.e. without mpi, for this specific case?
<div><br>
</div>
<div>If it does then there is probably an error in how you have linked/compiled the mpi versions. Please provide:</div>
<div><br>
</div>
<div>a) The mpi compiler you used.</div>
<div>b) Which type of mpi you are using (openmpi, mvapich, intel mpi etc)</div>
<div>c) The parallel compilation options.</div>
<div><br>
</div>
<div>N.B., a useful resource is <a href="https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor" title="https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor
Ctrl+Click or tap to follow the link" target="_blank">https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor</a></div>
<div><br>
</div>
<div>N.N.B., ulimit -s is not needed, this is (now) done in the software.</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jul 28, 2015 at 2:22 PM, Lan, Wangwei <span dir="ltr">
<<a href="mailto:wl13c@my.fsu.edu" target="_blank">wl13c@my.fsu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<p><span style="font-size:14pt">Dear Professor <span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif">Marks:</span></span></p>
<p><span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:15px"><br>
</span></p>
<p><span style="color:rgb(33,33,33); font-family:Corbel,sans-serif; font-size:14pt"><span style="font-family:Corbel,sans-serif">I've check everything you have mentioned, they are all fine, nevertheless it still don't work. I think the input files are ok since
I have no problem running in non-parallel mode. </span></span></p>
<p><span style="color:rgb(33,33,33); font-family:Corbel,sans-serif; font-size:14pt"><span style="font-family:Corbel,sans-serif">I tried to make the supercell smaller (2x1x1), then it works. However, I don't know why that happens. </span></span></p>
<p><span style="font-size:14pt">By the way, I have "ulimit -s unlimited " in my .bashrc file. I'v also </span><span style="font-size:14pt">a</span><span style="font-size:14pt">djusted the RKMAX and RMT before. </span></p>
<p><span style="font-size:14pt"><br>
</span></p>
<p><span style="font-size:14pt">Sincerely</span></p>
<p><span style="font-size:14pt">Wangwei Lan</span></p>
<p><span style="font-size:14pt"><br>
</span></p>
<br>
<br>
<div style="color:rgb(0,0,0)">
<hr style="display:inline-block; width:98%">
<div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b>
<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a> <<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a>> on behalf of Laurence
Marks <<a href="mailto:L-marks@northwestern.edu" target="_blank">L-marks@northwestern.edu</a>><br>
<b>Sent:</b> Tuesday, July 28, 2015 13:09<br>
<b>To:</b> A Mailing list for WIEN2k users<br>
<b>Subject:</b> Re: [Wien] Segmentation fault in Supercell Calculation</font>
<div> </div>
</div>
<div>
<div dir="ltr">You have what is called a "Segmentation Violation" which was detected by 4 of the nodes and they called an error handler which stopped the mpi job on all the CPU's.
<div><br>
</div>
<div>This is normally because you have an error of some sort in your input files, any of case.in0, case.clmsum (and clmup/dn if you are using spin polarized).</div>
<div><br>
</div>
<div>1) Check that you do not have overlapping spheres and/or other mistakes.</div>
<div>2) Check your error files, e.g. "cat *.error". Are any others (e.g. dstart.error) not empty? Did you ignore an error during setup?</div>
<div>3) Check the lapw0 output in case.output0* -- maybe shows what is wrong.</div>
<div><br>
</div>
<div>There are many possible sources, you have to find the specific one.</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jul 28, 2015 at 12:57 PM, Lan, Wangwei <span dir="ltr">
<<a href="mailto:wl13c@my.fsu.edu" target="_blank">wl13c@my.fsu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Dear WIEN2k user:</p>
<p><br>
</p>
<p>I am using wien2k_14.2 on CentOS release 5.8. ifort version 12.1.3 with MKL. </p>
<p><br>
</p>
<p><br>
</p>
<p>After generating a 2x2x1 supercell with 30 atoms, I tried to do the scf calculation. However, I got some errors. I'v attached it at the end of this email. My wien2k was installed correctly. It works well for other calculations. It also worked if I run non-parallel
calculation for supercell. I'v searched the mail-list, but can't find any solutions. Could you give me a hint on how to solve the problem? Thank you very much.</p>
<p><br>
</p>
<p><br>
</p>
<p>Sincerely </p>
<p>Wangwei Lan</p>
<p><br>
</p>
<p><span style="font-size:12pt"><br>
</span></p>
<p><span style="font-size:12pt">On lapw0.error shows:</span><br>
</p>
<p> </p>
<p><span style="font-size:12pt">'Unknown' - SIGSEGV</span><br>
</p>
<p><br>
</p>
<p><br>
</p>
<p>On super.dayfile shows:</p>
<p><br>
</p>
<p>Child id 0 SIGSEGV</p>
<p> Child id 8 SIGSEGV</p>
<p> Child id 18 SIGSEGV</p>
<p> Child id 23 SIGSEGV</p>
<p> Child id 17 SIGSEGV</p>
<div><br>
</div>
<div><br>
</div>
<p><br>
</p>
<p>On Screen shows:</p>
<p>w2k_dispatch_signal(): received: Segmentation fault</p>
<p>w2k_dispatch_signal(): received: Segmentation fault</p>
<p>w2k_dispatch_signal(): received: Segmentation fault</p>
<p>w2k_dispatch_signal(): received: Segmentation fault</p>
<p>w2k_dispatch_signal(): received: Segmentation fault</p>
<p>w2k_dispatch_signal(): received: Segmentation fault</p>
<p>w2k_dispatch_signal(): received: Segmentation fault</p>
<p>--------------------------------------------------------------------------</p>
<p>MPI_ABORT was invoked on rank 18 in communicator MPI_COMM_WORLD </p>
<p>with errorcode 451782144.</p>
<p><br>
</p>
<p>NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.</p>
<p>You may or may not see output from other processes, depending on</p>
<p>exactly when Open MPI kills them.</p>
<p>--------------------------------------------------------------------------</p>
<p>--------------------------------------------------------------------------</p>
<p>mpirun has exited due to process rank 18 with PID 26388 on</p>
<p>node <a href="http://corfu.magnet.fsu.edu" target="_blank">corfu.magnet.fsu.edu</a> exiting without calling "finalize". This may</p>
<p>have caused other processes in the application to be</p>
<p>terminated by signals sent by mpirun (as reported here).</p>
<p>--------------------------------------------------------------------------</p>
<p>[<a href="http://corfu.magnet.fsu.edu:26369" target="_blank">corfu.magnet.fsu.edu:26369</a>] 23 more processes have sent help message help-mpi-api.txt / mpi-abort</p>
<p>[<a href="http://corfu.magnet.fsu.edu:26369" target="_blank">corfu.magnet.fsu.edu:26369</a>] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages</p>
<p><br>
</p>
<p>> stop error</p>
<p><br>
</p>
<div><br>
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<span><font color="#888888"></font></span></div>
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-- <br>
<div>
<div dir="ltr">Professor Laurence Marks<br>
Department of Materials Science and Engineering<br>
Northwestern University<br>
<a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a>
<div>Corrosion in 4D: <a href="http://MURI4D.numis.northwestern.edu" target="_blank">
MURI4D.numis.northwestern.edu</a><br>
Co-Editor, Acta Cryst A<br>
"Research is to see what everybody else has seen, and to think what nobody else has thought"<br>
Albert Szent-Gyorgi</div>
</div>
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<span class="HOEnZb"><font color="#888888">
<div><br>
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-- <br>
<div>
<div dir="ltr">Professor Laurence Marks<br>
Department of Materials Science and Engineering<br>
Northwestern University<br>
<a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a>
<div>Corrosion in 4D: <a href="http://MURI4D.numis.northwestern.edu" target="_blank">
MURI4D.numis.northwestern.edu</a><br>
Co-Editor, Acta Cryst A<br>
"Research is to see what everybody else has seen, and to think what nobody else has thought"<br>
Albert Szent-Gyorgi</div>
</div>
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<span class="HOEnZb"><font color="#888888"></font></span></div>
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<span class="HOEnZb"><font color="#888888"><br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>
<div dir="ltr">Professor Laurence Marks<br>
Department of Materials Science and Engineering<br>
Northwestern University<br>
<a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a>
<div>Corrosion in 4D: <a href="http://MURI4D.numis.northwestern.edu" target="_blank">
MURI4D.numis.northwestern.edu</a><br>
Co-Editor, Acta Cryst A<br>
"Research is to see what everybody else has seen, and to think what nobody else has thought"<br>
Albert Szent-Gyorgi</div>
</div>
</div>
</font></span></div>
</div>
</div>
</div>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail_signature">
<div dir="ltr">Professor Laurence Marks<br>
Department of Materials Science and Engineering<br>
Northwestern University<br>
<a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a>
<div>Corrosion in 4D: <a href="http://MURI4D.numis.northwestern.edu" target="_blank">
MURI4D.numis.northwestern.edu</a><br>
Co-Editor, Acta Cryst A<br>
"Research is to see what everybody else has seen, and to think what nobody else has thought"<br>
Albert Szent-Gyorgi</div>
</div>
</div>
</div>
</div>
</div>
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