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
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Received on Mon Feb 26 2018 - 17:30:03 PST
