Thank you very much for the feedback. It was indeed a problem with the
hostname, which was not the same as in the /etc/hosts file.
Maria C. Milletti
Professor of Chemistry
503A Science Complex
Eastern Michigan University
(734) 487-1183
On Mon, Feb 26, 2018 at 8:04 PM, Kevin Keane <kkeane.sandiego.edu> wrote:
> Looking at the log file, it looks to me as if your name resolution is not
> working correctly. Can you resolve MCMErwin.local from the command line?
>
> Generally, anything that ends with .local can be problematic with name
> resolution; according to the RFCs, this TLD is only supposed to be used
> with mdns (Bonjour) domains. Macs can be particularly aggressive with that,
> but I have also seen problems with Windows and Linux.
>
>
> On Mon, Feb 26, 2018 at 2:04 PM, Maria Clelia Milletti <
> mmilletti.emich.edu>
> wrote:
>
> > Hello,
> >
> > I am trying to resolve a parallel install issue on a Mac OS 10.12
> >
> > I have deleted the previous Amber12 version and I have updated XCode to
> 9.2
> > and MacPorts to 2.4.2, gcc5.
> >
> > I have installed the serial version successfully.
> >
> > For the parallel installation I use mpich-3.2.1
> >
> > in $AMBERHOME/AmberTools/src ./configure_mpich gnu
> >
> > finishes with the messages
> >
> > [3]: Nothing to be done for 'install-exec-am'
> >
> > [3]: Nothing to be done for 'install-data-am'
> >
> > I do the following for the parallel install in $AMBERHOME
> >
> > ./configure -mpi gnu
> >
> > make install
> >
> > There are no error messages and finishes with 'installation is complete'
> >
> > When I test using
> >
> > export DO_PARALLEL="mpirun -np 2"
> >
> > make test
> >
> > every test fails.
> >
> > I have attached the .log file
> >
> >
> >
> > Thank you.
> >
> > Maria C. Milletti
> > Professor of Chemistry
> > 503A Science Complex
> > Eastern Michigan University
> > (734) 487-1183
> >
> > On Mon, Feb 26, 2018 at 4:24 PM, Maria Clelia Milletti <
> > mmilletti.emich.edu>
> > wrote:
> >
> > > Hello,
> > >
> > > I am trying to resolve a parallel install issue on a Mac OS 10.12
> > >
> > > I have deleted the previous Amber12 version and I have updated XCode to
> > > 9.2 and MacPorts to 2.4.2, gcc5.
> > >
> > >
> > >
> > > I do the following to install the serial version:
> > >
> > > In $AMBERHOME
> > >
> > > ./configure gnu
> > >
> > > source amber.sh
> > >
> > > make install
> > >
> > > make test
> > >
> > > All tests are PASSED
> > >
> > >
> > >
> > > For the parallel installation I use mpich-3.2.1
> > >
> > > in $AMBERHOME/AmberTools/src ./configure_mpich gnu
> > >
> > > finishes with the messages
> > >
> > > [3]: Nothing to be done for 'install-exec-am'
> > >
> > > [3]: Nothing to be done for 'install-data-am'
> > >
> > > Does that mean it worked?
> > >
> > >
> > >
> > > I do the following for the parallel install in $AMBERHOME
> > >
> > > ./configure -mpi gnu
> > >
> > > make install
> > >
> > > There are no error messages and finishes with 'installation is
> complete'
> > >
> > >
> > >
> > > When I test using
> > >
> > > export DO_PARALLEL="mpirun -np 2"
> > >
> > > make test
> > >
> > > every test fails.
> > >
> > > I have attached the .log files
> > >
> > >
> > >
> > > Thank you.
> > >
> > > Maria C. Milletti
> > > Professor of Chemistry
> > > 503A Science Complex
> > > Eastern Michigan University
> > > (734) 487-1183
> > >
> > > On Thu, Sep 21, 2017 at 1:35 PM, Maria Clelia Milletti <
> > > mmilletti.emich.edu> wrote:
> > >
> > >> 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-cha
> > >>> nnel-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
> > >>> >>>>>>>>
> > >>> >>>>>>>> _______________________________________________
> > >>> >>>>>>>> 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
> > >>>
> > >>> _______________________________________________
> > >>> 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
> >
> >
>
>
> --
>
> _______________________________________________________________________
> Kevin Keane | Systems Architect | University of San Diego ITS |
> kkeane.sandiego.edu
> Maher Hall, 192 |5998 Alcalá Park | San Diego, CA 92110-2492 |
> 619.260.6859
> <%28619%29%20260-2298>
> _______________________________________________
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Received on Mon Apr 02 2018 - 13:30:03 PDT
