Retried with "make -j 4 install" after installing a cuda 9.2 patch and
found the race condition returned. So, just don't use multiple threads for
make as previously advised.
Sincerely,
Dow
⚛Dow Hurst, Research Scientist
340 Sullivan Science Bldg.
Dept. of Chem. and Biochem.
University of North Carolina at Greensboro
PO Box 26170 Greensboro, NC 27402-6170
On Thu, Nov 1, 2018 at 12:23 AM Dow Hurst <dphurst.uncg.edu> wrote:
> I found "make -j 8 install" created the same problem, but "make -j 4
> install" worked.
> Sincerely,
> Dow
> ⚛Dow Hurst, Research Scientist
> 340 Sullivan Science Bldg.
> Dept. of Chem. and Biochem.
> University of North Carolina at Greensboro
> PO Box 26170 Greensboro, NC 27402-6170
>
>
>
> On Thu, May 10, 2018 at 3:34 PM Chris Neale <candrewn.gmail.com> wrote:
>
>> Dear David:
>>
>> indeed, removing the "-j 24" flag resolves the issue. Thank you very much
>> for your help.
>>
>> Chris.
>>
>> On Wed, May 9, 2018 at 6:20 AM, David A Case <david.case.rutgers.edu>
>> wrote:
>>
>> > On Tue, May 08, 2018, Chris Neale wrote:
>> > >
>> > > On a dgx-1, I can compile serial, serial+GPU, and MPI+GPU pmemd for
>> > > amber18, but I get a compile error for the straight MPI version.
>> >
>> > Thanks for the report.
>> > >
>> > > mpif90 -DBINTRAJ -DEMIL -DMPI -DSANDER -c -O3 -mtune=native -fPIC
>> > > -ffree-form -I/home/cneale/exec/AMBER/amber18/include
>> > > -I/home/cneale/exec/AMBER/amber18/include -I../sander \
>> > > -o transf.SANDER.o transf.F90
>> > > Fatal Error: Can't delete temporary module file 'memory_module.mod0':
>> No
>> > > such file or directory
>> >
>> > First: note that you are compiling pbsa here, not pmemd. My best
>> > initial guess is that no one has tested a parallel build with as many as
>> > 24 threads, and that you have hit a race condition: the pbsa component
>> > shares code with sander, and I'm guessing that the Makefiles don't
>> > recognize this cross-dependency. Simplest test would be to remove the
>> > "-j24" flag and see anything changes.
>> >
>> > If that doesn't help, make sure that the mpif90 command above is doing
>> > what you want, i.e. type "mpif90 -show".
>> >
>> > ...regards....dac
>> >
>> >
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
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>>
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Received on Wed Oct 31 2018 - 23:00:02 PDT
