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
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> 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
> >>>> _______________________________________________
> >>>> 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
> >> _______________________________________________
> >> 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
>
> _______________________________________________
> 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
Received on Thu Sep 21 2017 - 07:00:02 PDT
