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Dear Grigory,<br>
<br>
<div class="moz-cite-prefix">On 31/01/14 19:08, Grigory Shamov
wrote:<br>
</div>
<blockquote
cite="mid:CF114E5A.2E92E%25Grigory.Shamov@ad.umanitoba.ca"
type="cite">
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<div>Dear Manhui,</div>
<div><br>
</div>
<div>Thank you for the reply. We have 48GB or 96GB RAM nodes,
always with 47GB swap partition. The memory should be allocated
by Torque accordingly to user's request. If he uses more memory
in MolPro than requested from the batch queuing system, the job
gets terminated automatically ( a different kind of error to
see, for getting SIGTERM, and the event logged for us).</div>
<div><br>
</div>
<div>The particular job ran on four 48GB nodes, four processes
each (3 compute, 1 data server as it was SF version) and
requested 98 GB of RAM — which is not enough, but the job didn't
reach the state of being killed for using too much, but just
failed to allocate, right?</div>
</blockquote>
Yes, it appeared you requested too much memory.<br>
<blockquote
cite="mid:CF114E5A.2E92E%25Grigory.Shamov@ad.umanitoba.ca"
type="cite">
<div><br>
</div>
<div>SHMMAX is a per-node value for SystemV shared memory. Some
old versions of GA used to depend on it. I should've think that
for using SF it is irrelevant, unless MolPro uses also SystemV
internally. <br>
</div>
</blockquote>
For pure MPI-2 version of parallel Molpro, SHMMAX is irrelevant.<br>
<blockquote
cite="mid:CF114E5A.2E92E%25Grigory.Shamov@ad.umanitoba.ca"
type="cite">
<div><br>
</div>
<div>On the other hand we do not allow for virtual memory
overcommit. Could MolPro want to allocate a large Virtual
memory, much larger than the Residential memory ?</div>
</blockquote>
Molpro uses c/c++ allocation functions, and the OS determines how to
allocate the memory. However, even if the OS can allocate large
virtual memory for Molpro, the job will probably hang up or die due
to poor performance of virtual memory.<br>
<br>
Best wishes,<br>
Manhui <br>
<blockquote
cite="mid:CF114E5A.2E92E%25Grigory.Shamov@ad.umanitoba.ca"
type="cite">
<div><br>
</div>
<div>
<div>
<div>
<div>-- </div>
<div>Grigory Shamov</div>
</div>
<div>HPC Analyst, Westgrid/Compute Canada</div>
<div>E2-588 EITC Building, University of Manitoba</div>
<div>(204) 474-9625</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<div><br>
</div>
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<span style="font-weight:bold">From: </span>Manhui Wang <<a
moz-do-not-send="true" href="mailto:wangm9@cardiff.ac.uk">wangm9@cardiff.ac.uk</a>><br>
<span style="font-weight:bold">Date: </span>Friday, 31
January, 2014 12:03 PM<br>
<span style="font-weight:bold">To: </span>Grigory Shamov <<a
moz-do-not-send="true"
href="mailto:Grigory.Shamov@umanitoba.ca">Grigory.Shamov@umanitoba.ca</a>><br>
<span style="font-weight:bold">Cc: </span>"<a
moz-do-not-send="true" href="mailto:molpro-user@molpro.net">molpro-user@molpro.net</a>"
<<a moz-do-not-send="true"
href="mailto:molpro-user@molpro.net">molpro-user@molpro.net</a>><br>
<span style="font-weight:bold">Subject: </span>Re:
[molpro-user] gmainv1 failure to allocate - what to do?<br>
</div>
<div><br>
</div>
<div>
<div bgcolor="#FFFFFF" text="#000000">Dear Grigory,<br>
<br>
<div class="moz-cite-prefix">On 31/01/14 15:07, Grigory
Shamov wrote:<br>
</div>
<blockquote
cite="mid:CF111858.2E8F0%25Grigory.Shamov@ad.umanitoba.ca"
type="cite">
<pre wrap="">Dear MolPro users,
I have compiled MolPro with Intel 12 and auto-built MVAPICH2. (I had to
substitute MVAPICH2-2.0b instead of the unavailable tar ball of
MVAPICH2-1.9 in the processs; also to decrease optimization to -O2; I
attach my CONFIG. I understand it picked I8 array indexes, right?).
When our user ran it on a large task, with -m 1000m he got the following
error:
Multipassing necessary in transformation. To avoid, increase memory by
3561.33 Mwords.
? Error
? 2-ext paging plus 3-ext ints not yet working (kintb)!
? The problem occurs in cckint
Then, I told him to increase the memory, but with -m 4600m it fails in a
different way:
gmainv1 failure to allocate 4600230002
gmainv1 failure to allocate 4600230002
gmainv1 failure to allocate 4600230002
gmainv1 failure to allocate 4600230002</pre>
</blockquote>
How much memory does the machine have? If you want to run
Molpro job with <br>
-m 4600m <b>with 4 processes</b>, actually you are
requesting 4600*1000000 words(1 word = 8 bytes) per process.<br>
The total requested memory is 137 GB (4600*1000000 * 8 * 4).<br>
<blockquote
cite="mid:CF111858.2E8F0%25Grigory.Shamov@ad.umanitoba.ca"
type="cite">
<pre wrap="">I've googled this problem, and have seen some answers related to SHMMAX
value. On our cluster we have it increase though:
cat /proc/sys/kernel/shmmax
68719476736</pre>
</blockquote>
This is around 64GB.<br>
<br>
Could you please check if the requested memory exceeds the
hard memory limit on the machine?<br>
<br>
<br>
Best wishes,<br>
Manhui<br>
<blockquote
cite="mid:CF111858.2E8F0%25Grigory.Shamov@ad.umanitoba.ca"
type="cite">
<pre wrap="">Could you please suggest, how does one avoid this problem,? Also, I did
use the default limits when compiling (number of atoms etc.) -- if that is
the reason, which limits should be increased? Thank you very much!
</pre>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Molpro-user mailing list
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:Molpro-user@molpro.net">Molpro-user@molpro.net</a><a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.molpro.net/mailman/listinfo/molpro-user">http://www.molpro.net/mailman/listinfo/molpro-user</a></pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
-----------
Manhui Wang
School of Chemistry, Cardiff University,
Main Building, Park Place,
Cardiff CF10 3AT, UK
</pre>
</div>
</div>
</span>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
-----------
Manhui Wang
School of Chemistry, Cardiff University,
Main Building, Park Place,
Cardiff CF10 3AT, UK
</pre>
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