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
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> 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
> >>>> 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
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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- application/octet-stream attachment: test.out
Received on Wed Sep 20 2017 - 13:30:02 PDT
