<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>No. I had an fftw build from before that I reused and instructed gromacs to use.</div><div><br></div><div>Erik</div><div><br><div><div>On 5 Apr 2013, at 13:08, Rossen Apostolov <<a href="mailto:rossen@kth.se">rossen@kth.se</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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Hi Erik,<br>
<br>
Are you compiling fftw with the build, i.e. using
-DGMX_BUILD_OWN_FFTW ?<br>
<br>
Cheers,<br>
Rossen<br>
<br>
<div class="moz-cite-prefix">On 4/5/13 11:55 AM, Erik Marklund
wrote:<br>
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Hi,
<div><br>
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<div>Building gromacs 4.6.1 failed whenever I issued parallel
make, i.e. make -j. I reported this to the cluster admins since
I had never seen such behaviour before from gromacs' side, and
here's their reply. I can't tell whether gromacs is at fault or
the cluster.</div>
<div><br>
</div>
<div>Erik<br>
<div><br>
<div>Begin forwarded message:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite"><span style="font-family: Helvetica;
font-size: medium; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: 2; text-align: -webkit-auto;
text-indent: 0px; text-transform: none; white-space:
normal; widows: 2; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0px; display: inline !important; float: none; "> Hi,</span><br style="font-family: Helvetica; font-size: medium;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-align: -webkit-auto; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; ">
<br style="font-family: Helvetica; font-size: medium;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-align: -webkit-auto; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; ">
<blockquote type="cite" style="font-family: Helvetica;
font-size: medium; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: 2; text-align: -webkit-auto;
text-indent: 0px; text-transform: none; white-space:
normal; widows: 2; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0px; ">I was compiling gromacs on tintin's login node the
other day and it<br>
seems that parallel make, i.e. make -j, doesn't work on
tintin. I<br>
got linker errors that never showed up when make was run
serially.<br>
I've never encountered such behaviour before.<br>
</blockquote>
<br style="font-family: Helvetica; font-size: medium;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-align: -webkit-auto; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; ">
<span style="font-family: Helvetica; font-size: medium;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-align: -webkit-auto; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline
!important; float: none; ">Without any more information
(or being able to look for actual files right now), I'd
guess this is a problem with the makefiles rather than the
actual make. It seems somewhat unexpected that CMake would
create makefiles that aren't safe for parallel building,
but it does seem the most likely culprit (assuming it
doesn't let developers add rules directly to the makefile
to work around problems, I don't remember if that's
possible).</span><br style="font-family: Helvetica;
font-size: medium; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: 2; text-align: -webkit-auto;
text-indent: 0px; text-transform: none; white-space:
normal; widows: 2; word-spacing: 0px;
-webkit-text-size-adjust: auto; -webkit-text-stroke-width:
0px; ">
<br style="font-family: Helvetica; font-size: medium;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-align: -webkit-auto; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; ">
<span style="font-family: Helvetica; font-size: medium;
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-align: -webkit-auto; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; -webkit-text-size-adjust: auto;
-webkit-text-stroke-width: 0px; display: inline
!important; float: none; ">That you only see the problem
on tintin can likely be explained by timing or other non
deterministic factors.</span></blockquote>
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