attached.
Maria C. Milletti
Professor of Chemistry
503A Science Complex
Eastern Michigan University
(734) 487-1183
On Wed, Sep 20, 2017 at 4:44 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> I would have to see the output.
>
> Bill
>
>
> On 9/20/17 1:13 PM, Maria Clelia Milletti wrote:
> > it seems to work fine. I've attached the test.out file.
> > Any thoughts as to why when I make test after ./configure -mpi gnu every
> > test fails?
> > thanks,
> >
> > Maria C. Milletti
> > Professor of Chemistry
> > 503A Science Complex
> > Eastern Michigan University
> > (734) 487-1183
> >
> > On Wed, Sep 20, 2017 at 3:33 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> Try with a semicolon:
> >>
> >> $ DO_PARALLEL='mpirun -n 2' ; ./RunTest.sh
> >>
> >> Bill
> >>
> >>
> >> On 9/20/17 12:30 PM, Maria Clelia Milletti wrote:
> >>> It does not. The command returns what looks like a prompt (>) and stays
> >>> suspended that way, but no output is written to test.out in the
> >>> Test_Parallel folder.
> >>>
> >>> Maria C. Milletti
> >>> Professor of Chemistry
> >>> 503A Science Complex
> >>> Eastern Michigan University
> >>> (734) 487-1183
> >>>
> >>> On Tue, Sep 19, 2017 at 1:26 PM, Daniel Roe <daniel.r.roe.gmail.com>
> >> wrote:
> >>>> 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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> >>>>>>>>
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> >>>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> -------------------------
> >>>>>> 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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> >>>>>>
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> >>>>
> >>>> --
> >>>> -------------------------
> >>>> 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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> >>>>
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> >>
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> >>
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Received on Wed Sep 20 2017 - 14:00:04 PDT
