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
Received on Wed Sep 20 2017 - 13:00:03 PDT
