Dan and Bill,
the 'mpirun -n 2 echo Hello' command returns Hello twice, as expected.
In addition, 'which mpirun' returns /Applications/Amber17/amber16/bin/mpirun,
also as expected.
Maria
Maria C. Milletti
Professor of Chemistry
503A Science Complex
Eastern Michigan University
(734) 487-1183
On Thu, Sep 21, 2017 at 12:57 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Can you run any other MPI jobs on that machine? E.g. if there's a 'hello
> world' sort of test you can run. If MPI in general is broken, then the
> MPI community may be your best bet.
>
> I would search on the error msgs for clues, e.g.
>
> https://serverfault.com/questions/648317/intel-mpi-
> gives-channel-initialization-failed-error-mpirun
>
> Bill
>
>
> On 9/21/17 6:54 AM, Maria Clelia Milletti wrote:
> > Yes, I did
> > $ export DO_PARALLEL='mpirun -n 2'
> > before 'make test'.
> > I've used the same procedure for two other MacPro's and it worked fine,
> so
> > I'm not sure what went wrong with this machine.
> > I've attached the config.log file for mpich.3-2. It exits 0, so I thought
> > everything was fine.
> > Is there anything else I can look at to see where the problem originates?
> >
> > Maria C. Milletti
> > Professor of Chemistry
> > 503A Science Complex
> > Eastern Michigan University
> > (734) 487-1183
> >
> > On Wed, Sep 20, 2017 at 7:49 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> >> Looks like your MPI environment isn't set up. I've never used it myself.
> >>
> >> Fatal error in MPI_Init: Other MPI error, error stack:
> >> MPIR_Init_thread(474)..............:
> >> MPID_Init(190).....................: channel initialization failed
> >> MPIDI_CH3_Init(89).................:
> >> MPID_nem_init(320).................:
> >> MPID_nem_tcp_init(173).............:
> >> MPID_nem_tcp_get_business_card(420):
> >> MPID_nem_tcp_init(379).............: gethostbyname failed,
> >> MCMErwin.local (errno 1)
> >> ./Run.sff: Program error
> >>
> >> Maybe if you did
> >>
> >> $ export DO_PARALLEL='mpirun -n 2'
> >>
> >> before 'make test', it would work.
> >>
> >> On 9/20/17 1:54 PM, Maria Clelia Milletti wrote:
> >>> 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
> >>>>>>>>>>>>
> >>>>>>>>>>>>
> >>>>>>>>>>>> _______________________________________________
> >>>>>>>>>>>> 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
> >>>>>>>>
> >>>>>>>> _______________________________________________
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> >>>>>>>>
> >>>>>>> _______________________________________________
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> >>>>>>
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Received on Thu Sep 21 2017 - 11:00:02 PDT
