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
>>>
>>
>>
>
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Received on Mon Feb 26 2018 - 14:30:03 PST
