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
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>>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> -------------------------
>>>>>>>>>> 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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>>>>>>>>>> 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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Received on Thu Sep 21 2017 - 10:00:03 PDT
