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
>>>>>>>>
>>>>>>>>
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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 mailing list
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>>>>> 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 - 14:00:02 PDT
