<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p>Hi Gavin,</p>
<p><br>
</p>
<p> Thank you very much. You are right, I was using -lmkl_blacs_intelmpi_lp64 instead of <span style="font-family: Calibri, Arial, Helvetica, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">-lmkl_blacs_openmpi_lp64.</span></p>
<p><span style="font-family: Calibri, Arial, Helvetica, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">I have recompiled and it is working now.</span></p>
<p><span style="font-family: Calibri, Arial, Helvetica, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;"><br>
</span></p>
<p><span style="font-family: Calibri, Arial, Helvetica, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">Thanks again,</span></p>
<p><span style="font-family: Calibri, Arial, Helvetica, sans-serif, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">Fhokrul</span></p>
<br>
<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 <wien-bounces@zeus.theochem.tuwien.ac.at> on behalf of Gavin Abo <gsabo@crimson.ua.edu><br>
<b>Sent:</b> Thursday, June 23, 2016 1:59 AM<br>
<b>To:</b> A Mailing list for WIEN2k users<br>
<b>Subject:</b> Re: [Wien] Running parallel job with Slurm+intel mpi</font>
<div> </div>
</div>
<div>
<div class="moz-cite-prefix">SIGSEGV errors can be not easy to solve, because they can have many possible causes:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.democritos.it/pipermail/pw_forum/2005-March/002272.html" id="LPlnk441119">http://www.democritos.it/pipermail/pw_forum/2005-March/002272.html</a><br>
<a class="moz-txt-link-freetext" href="http://software.intel.com/en-us/articles/determining-root-cause-of-sigsegv-or-sigbus-errors/" title="http://software.intel.com/en-us/articles/determining-root-cause-of-sigsegv-or-sigbus-errors/
Ctrl+Click or tap to follow the link">http://software.intel.com/en-us/articles/determining-root-cause-of-sigsegv-or-sigbus-errors/</a><br>
<br>
However, maybe the cause is the same as a similar case that occurred before where the error occurred when -lmkl_blacs_lp64 was used when -lmkl_blacs_openmpi_lp64 should have been used instead for Open MPI [
<a class="moz-txt-link-freetext" href="http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12746.html">
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12746.html</a> ].<br>
<br>
What blacs did you use in your parallel compiler options (for RP_LIB) when you compiled WIEN2k using Open MPI?<br>
<br>
On 6/22/2016 7:30 AM, Md. Fhokrul Islam wrote:<br>
</div>
<blockquote type="cite">
<div id="divtagdefaultwrapper" style="font-size:12pt; color:#000000; background-color:#FFFFFF; font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi Prof Blaha,</p>
<p><br>
</p>
<p> I have compiled MPI version of Wien2k_14.2 with OpenMPI <span style="font-size:12pt">and have got all </span><span style="font-size:12pt">MPI executables. </span></p>
<p><span style="font-size:12pt">But when I run a test calculation using 4 </span>
<span style="font-size:12pt">cores</span><span style="font-size:12pt">, I get the the </span><span style="font-size:12pt">following error message. Could you</span></p>
<p><span style="font-size:12pt">please let me know what should I do to fix this problem. </span></p>
<p><br>
</p>
<p>case.dayfile</p>
<p><br>
</p>
<div> start (Tue Jun 21 20:57:01 CEST 2016) with lapw0 (100/99 to go)</div>
<div><br>
</div>
<div> cycle 1 (Tue Jun 21 20:57:01 CEST 2016) (100/99 to go)</div>
<div><br>
</div>
<div>> lapw0 -p (20:57:01) starting parallel lapw0 at Tue Jun 21 20:57:02 CEST 2016</div>
<div>-------- .machine0 : 4 processors</div>
<div>4.684u 0.733s 0:04.50 120.2% 0+0k 220432+4688io 78pf+0w</div>
<div>> lapw1 -up -p -c (20:57:06) starting parallel lapw1 at Tue Jun 21 20:57:06 CEST 2016</div>
<div>-> starting parallel LAPW1 jobs at Tue Jun 21 20:57:06 CEST 2016</div>
<div>running LAPW1 in parallel mode (using .machines)</div>
<div>1 number_of_parallel_jobs</div>
<div> au063 au063 au063 au063(47) Child id 3 SIGSEGV</div>
<div> Child id 0 SIGSEGV</div>
<div> Child id 1 SIGSEGV</div>
<div> Child id 2 SIGSEGV</div>
<div>--------------------------------------------------------------------------</div>
<div>MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD</div>
<div>with errorcode 1543169252.</div>
<div><br>
</div>
<br>
<p>Error file:</p>
<p><br>
</p>
<div>LAPW0 END</div>
<div>w2k_dispatch_signal(): received: Segmentation fault</div>
<div>w2k_dispatch_signal(): received: Segmentation fault</div>
<div>w2k_dispatch_signal(): received: Segmentation fault</div>
<div>w2k_dispatch_signal(): received: Segmentation fault</div>
<div>[au063:29993] 3 more processes have sent help message help-mpi-api.txt / mpi-abort</div>
<div>[au063:29993] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages</div>
<div><br>
</div>
<br>
<p>Thanks,</p>
<p>Fhokrul</p>
<p><br>
</p>
<p><br>
</p>
<br>
<br>
<div style="color:rgb(0,0,0)">
<div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Wien
<a class="moz-txt-link-rfc2396E" href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at">
<wien-bounces@zeus.theochem.tuwien.ac.at></a> on behalf of Peter Blaha <a class="moz-txt-link-rfc2396E" href="mailto:pblaha@theochem.tuwien.ac.at">
<pblaha@theochem.tuwien.ac.at></a><br>
<b>Sent:</b> Monday, June 13, 2016 8:54 AM<br>
<b>To:</b> A Mailing list for WIEN2k users<br>
<b>Subject:</b> Re: [Wien] Running parallel job with Slurm+intel mpi</font>
<div> </div>
</div>
</div>
<font size="2"><span style="font-size:10pt">
<div class="PlainText">No, the srun command cannot work with these options, but need other
<br>
switches.<br>
Most likely in WIEN2k_14.2 you will have to use mpirun, or try:<br>
<br>
srun -n_NP_ (i.e. without the blank between n and _NP_)<br>
<br>
<br>
In the next version, we will have support for srun, but at least for <br>
mixed k-point+mpi-support it requires also a small change in the <br>
lapw*para scripts.<br>
<br>
<br>
<br>
On 06/09/2016 04:29 PM, Md. Fhokrul Islam wrote:<br>
> Dear Wien2k users,<br>
><br>
><br>
> I am trying to do some calculation with a large system with mpi<br>
> version but having problem with<br>
><br>
> running the job. I have compiled Wien2k 14.2 with intel libraries and<br>
> have generated all mpi executables.<br>
><br>
> But our system requires us to use srun instead of mpirun. So I have<br>
> changed parallel options to<br>
><br>
><br>
> srun -n _NP_ -machinefile _HOSTS_ _EXEC_.<br>
><br>
><br>
> I also have tried other options that I saw in the mailing list<br>
><br>
><br>
> srun -n _NP_<br>
><br>
><br>
> but that didn't work. No new files are created and the dayfile is stuck<br>
><br>
> in lapw0.<br>
><br>
><br>
> case.dayfile:<br>
> ----------------------------------<br>
> Calculating GaAs in /lunarc/nobackup/users/eishfh/WIEN2k/test/GaAs<br>
> on au054 with PID 189944<br>
> using WIEN2k_14.2 (Release 15/10/2014) in<br>
> /lunarc/nobackup/users/eishfh/SRC/Wien2k14.2-mpi<br>
><br>
><br>
> start (Thu Jun 9 13:14:39 CEST 2016) with lapw0 (100/99 to go)<br>
><br>
> cycle 1 (Thu Jun 9 13:14:39 CEST 2016) (100/99 to go)<br>
><br>
> > lapw0 -p (13:14:39) starting parallel lapw0 at Thu Jun 9<br>
> 13:14:39 CEST 2016<br>
> -------- .machine0 : 4 processors<br>
> -------------------<br>
><br>
><br>
> I understood from the userguide that the -p option in runsp_lapw picks up<br>
><br>
> mpi version depending on the form of the .machines file. Here is the<br>
><br>
> .machines file that I have used for this test calculation.<br>
><br>
><br>
> #<br>
> lapw0:au165 au165 au165 au165<br>
> 1:au165 au165 au165 au165<br>
> granularity:1<br>
> extrafine:1<br>
> lapw2_vector_split:2<br>
><br>
> So I am wondering if anyone can tell me how can I fix the problem.<br>
><br>
> Thanks,<br>
><br>
> Fhokrul<br>
><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Wien mailing list<br>
> <a class="moz-txt-link-abbreviated" href="mailto:Wien@zeus.theochem.tuwien.ac.at">
Wien@zeus.theochem.tuwien.ac.at</a><br>
> <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" id="LPlnk527074">
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a>
<div id="LPBorder_GT_14666011401310.3932420394752014" style="margin-bottom:20px; overflow:auto; width:100%; text-indent:0px" contenteditable="false">
<table id="LPContainer_14666011401220.3377222606458159" cellspacing="0" style="width:90%; overflow:auto; padding-top:20px; padding-bottom:20px; margin-top:20px; border-top-width:1px; border-top-style:dotted; border-top-color:rgb(200,200,200); border-bottom-width:1px; border-bottom-style:dotted; border-bottom-color:rgb(200,200,200); background-color:rgb(255,255,255)">
<tbody>
<tr valign="top" style="border-spacing:0px">
<td id="TextCell_14666011401260.44635978717927016" colspan="2" style="vertical-align:top; padding:0px; display:table-cell">
<div id="LPTitle_14666011401260.07450109101694036" style=""><a id="LPUrlAnchor_14666011401280.26770733641546407" href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" target="_blank" style="text-decoration:none">Wien -- A Mailing list for WIEN2k users</a></div>
<div id="LPMetadata_14666011401280.27608741457236086" style="">zeus.theochem.tuwien.ac.at</div>
<div id="LPDescription_14666011401290.9744229272922187" style="display:block; color:rgb(102,102,102); font-weight:normal; font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif; font-size:14px; line-height:20px; max-height:100px; overflow:hidden">
A Mailing list for WIEN2k users. Please post questions, suggestions or comments about WIEN2k ONLY in this list. Please follow the following "Nettiquette" (depending ...</div>
</td>
</tr>
</tbody>
</table>
</div>
<br>
<br>
> SEARCH the MAILING-LIST at: <a href="http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html">
</a><a class="moz-txt-link-freetext" href="http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html">http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html</a><br>
><br>
<br>
-- <br>
<br>
P.Blaha<br>
--------------------------------------------------------------------------<br>
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna<br>
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982<br>
Email: <a class="moz-txt-link-abbreviated" href="mailto:blaha@theochem.tuwien.ac.at">
blaha@theochem.tuwien.ac.at</a> WIEN2k: <a href="http://www.wien2k.at"></a><a class="moz-txt-link-freetext" href="http://www.wien2k.at">http://www.wien2k.at</a><br>
WWW: <a href="http://www.imc.tuwien.ac.at/staff/tc_group_e.php">http://www.imc.tuwien.ac.at/staff/tc_group_e.php</a><br>
--------------------------------------------------------------------------<br>
</div>
</span></font></div>
</div>
</blockquote>
</div>
</div>
</div>
</body>
</html>