OK - in that case the next step would be to try testing an individual program.
$ cd $AMBERHOME/AmberTools/src/cpptraj/test/Test_Parallel
$ DO_PARALLEL='mpirun -n 2' ./RunTest.sh
See if that succeeds.
-Dan
On Tue, Sep 19, 2017 at 11:53 AM, Maria Clelia Milletti
<mmilletti.emich.edu> wrote:
> I do get
> Hello
> Hello
>
> Maria C. Milletti
> Professor of Chemistry
> 503A Science Complex
> Eastern Michigan University
> (734) 487-1183
>
> On Tue, Sep 19, 2017 at 10:42 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> The errors in your log have to do with MPI, not with Amber itself. Are
>> you able to use MPI to run a program at all? E.g.
>>
>> mpirun -n 2 echo Hello
>>
>> If the output is not just:
>>
>> Hello
>> Hello
>>
>> then there is something wrong with the MPI installation on your machine.
>>
>> -Dan
>>
>> On Tue, Sep 19, 2017 at 10:35 AM, Maria Clelia Milletti
>> <mmilletti.emich.edu> wrote:
>> > Thank you, that worked.
>> > I am now trying to install the parallel version on a different machine,
>> > older but also a 12-core MacPro running OS 12.10.6
>> > The ./configure -mpi gnu in $AMBERHOME is successful, but when I 'make
>> > test', every test fails. I have attached the diff and log files.
>> > Any help is greatly appreciated.
>> >
>> > Maria C. Milletti
>> > Professor of Chemistry
>> > 503A Science Complex
>> > Eastern Michigan University
>> > (734) 487-1183
>> >
>> > On Mon, Sep 18, 2017 at 4:33 PM, David A Case <david.case.rutgers.edu>
>> > wrote:
>> >
>> >> On Mon, Sep 18, 2017, Maria Clelia Milletti wrote:
>> >>
>> >> > I'm having a problem installing the parallel version of
>> >> > Amber16/AmberTools17 on a 12-core Intel XeonE5 MacPro (OS 10.12.6).
>> >> > The serial installation was successful. I then downloaded mpich-3.2
>> and
>> >> > installed it from the AmberTools/src directory using the command
>> >> > ./configure_mpich gnu
>> >>
>> >> > When I try to 'make test' I get the error
>> >> > No rule to make target 'test'.
>> >>
>> >> What directory are you in when you issue this command? Note that, after
>> >> running configure_mpich, you need to go back to $AMBERHOME, re-run
>> >> configure
>> >> with the "-mpi" option, then type "make install" followed by "make
>> test".
>> >>
>> >> ....dac
>> >>
>> >>
>> >> _______________________________________________
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>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
>> _______________________________________________
>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Sep 19 2017 - 10:30:06 PDT
