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
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>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
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>>>>>>>> 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 Wed Sep 20 2017 - 17:00:03 PDT
