[gmx-users] Fwd: make check error

[Anna Lappala]

> Hi,
> 
> please decrypt what you said- it was obvious from my earlier steps that i am making gromacs with mpi support. Again, what is it if not mpirun? How do i check all this? 
>> "it wants you to choose multiple ranks, before you can use the
>> aforementioned CMake options to describe to ctest how to use it."
> No, all it "wants" is to locate mpirun in any of the aforementioned folders. The tests run successfully if i put mpirun executable in the folder it wants to. 
> This does not however change the situation when i rerun the cmake command. 
> So let me be more clear. What do i do to make mpirun and which one of the steps that i am doing is wrong? See the commands in previous emails.
> 
>> On Oct 21, 2016, at 01:47, Mark Abraham <mark.j.abraham at gmail.com> wrote:
>> 
>> Hi,
>> 
>> Assuming you are actually building GROMACS to run with MPI support, you
>> have a command that will be used to run an MPI program. Often that is
>> called mpirun, but not always. You need to find out what that is, and how
>> it wants you to choose multiple ranks, before you can use the
>> aforementioned CMake options to describe to ctest how to use it.
>> 
>> Mark
>> 
>>> On Fri, Oct 21, 2016 at 1:25 AM Anna Vernon <lappala.anna at gmail.com> wrote:
>>> 
>>> err, it does not find mpirun? I am confused
>>> 
>>> Test project /home/anna/Downloads/gromacs-2016/build
>>>    Start 21: MdrunMpiTests
>>> Could not find executable /home/anna/Downloads/gromacs-2016/build/mpirun
>>> Looked in the following places:
>>> /home/anna/Downloads/gromacs-2016/build/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/Release/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/Release/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/Debug/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/Debug/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/MinSizeRel/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/MinSizeRel/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/RelWithDebInfo/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/RelWithDebInfo/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/Deployment/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/Deployment/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/Development/mpirun
>>> /home/anna/Downloads/gromacs-2016/build/Development/mpirun
>>> home/anna/Downloads/gromacs-2016/build/mpirun
>>> home/anna/Downloads/gromacs-2016/build/mpirun
>>> home/anna/Downloads/gromacs-2016/build/Release/mpirun
>>> home/anna/Downloads/gromacs-2016/build/Release/mpirun
>>> home/anna/Downloads/gromacs-2016/build/Debug/mpirun
>>> home/anna/Downloads/gromacs-2016/build/Debug/mpirun
>>> home/anna/Downloads/gromacs-2016/build/MinSizeRel/mpirun
>>> home/anna/Downloads/gromacs-2016/build/MinSizeRel/mpirun
>>> home/anna/Downloads/gromacs-2016/build/RelWithDebInfo/mpirun
>>> home/anna/Downloads/gromacs-2016/build/RelWithDebInfo/mpirun
>>> home/anna/Downloads/gromacs-2016/build/Deployment/mpirun
>>> home/anna/Downloads/gromacs-2016/build/Deployment/mpirun
>>> home/anna/Downloads/gromacs-2016/build/Development/mpirun
>>> home/anna/Downloads/gromacs-2016/build/Development/mpirun
>>> Unable to find executable: /home/anna/Downloads/gromacs-2016/build/mpirun
>>> 1/1 Test #21: MdrunMpiTests ....................***Not Run   0.00 sec
>>> 
>>> 0% tests passed, 1 tests failed out of 1
>>> 
>>> Label Time Summary:
>>> MpiIntegrationTest    =   0.00 sec
>>> 
>>> Total Test time (real) =   0.00 sec
>>> 
>>> The following tests FAILED:
>>>     21 - MdrunMpiTests (Not Run)
>>> Errors while running CTest
>>> 
>>> 
>>>> On 20 October 2016 at 16:27, Anna Vernon <lappala.anna at gmail.com> wrote:
>>>> 
>>>> after doing this:
>>>> cmake .. -DMPIEXEC=mpirun -DMPIEXEC_NUMPROC_FLAG=-np -DNUMPROC=2,
>>>> -DNUMPROC=3, -DNUMPROC=4, -DNUMPROC=5, -DNUMPROC=6,
>>> -DNUMPROC=7,-DNUMPROC=8
>>>> make
>>>> make check
>>>> I get this:
>>>> The following tests FAILED:
>>>>     21 - MdrunMpiTests (Not Run)
>>>>     26 - regressiontests/pdb2gmx (Failed)
>>>> Errors while running CTest
>>>> CMakeFiles/run-ctest.dir/build.make:49: recipe for target
>>>> 'CMakeFiles/run-ctest' failed
>>>> make[3]: *** [CMakeFiles/run-ctest] Error 8
>>>> CMakeFiles/Makefile2:960: recipe for target
>>> 'CMakeFiles/run-ctest.dir/all'
>>>> failed
>>>> make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2
>>>> CMakeFiles/Makefile2:936: recipe for target 'CMakeFiles/check.dir/rule'
>>>> failed
>>>> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
>>>> Makefile:544: recipe for target 'check' failed
>>>> make: *** [check] Error 2
>>>> 
>>>> 
>>>> On 20 October 2016 at 15:40, Mark Abraham <mark.j.abraham at gmail.com>
>>>> wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> It'd be great to be able to make all things clear to all people, but one
>>>>> person's clarity is another's verbosity :-( But do see
>>>>> http://manual.gromacs.org/documentation/2016/install-guide/
>>>>> index.html#using-cmake-command-line-options
>>>>> .
>>>>> 
>>>>> Is an example of "cmake -DMPIEXEC=mpirun -DMPIEXEC_NUMPROC_FLAG=-np
>>>>> -DNUMPROC=6..." more clear, given that many people will want to
>>> customise
>>>>> at least one value?
>>>>> 
>>>>> Mark
>>>>> 
>>>>>> On Thu, 20 Oct 2016 23:29 Anna Vernon <lappala.anna at gmail.com> wrote:
>>>>>> 
>>>>>> hi
>>>>>> 
>>>>>> This passage (the one of interest in my case) of documentation is
>>>>> cryptic:
>>>>>> 
>>>>>> 
>>>>>> The make check target also runs integration-style tests that may run
>>>>> with
>>>>>> MPI if GMX_MPI=ON was set. To make these work, you may need to set the
>>>>>> CMake variables MPIEXEC, MPIEXEC_NUMPROC_FLAG, NUMPROC,
>>> MPIEXEC_PREFLAGS
>>>>>> and MPIEXEC_POSTFLAGS so that mdrun-mpi-test_mpi would run on multiple
>>>>>> ranks via the shell command
>>>>>> 
>>>>>> ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROC} ${MPIEXEC_PREFLAGS} \
>>>>>>      mdrun-mpi-test_mpi ${MPIEXEC_POSTFLAGS} -otherflags
>>>>>> 
>>>>>> Typically, one might use variable values mpirun, -np, 2, '', ''
>>>>>> respectively, in order to run on two ranks.
>>>>>> Is it possible to explain this more clearly? there are gazillions of
>>>>> files
>>>>>> in the cmake folder; where do I actually add the bit of code that sets
>>>>> the
>>>>>> variables?
>>>>>> 
>>>>>> On 20 October 2016 at 07:56, Mark Abraham <mark.j.abraham at gmail.com>
>>>>>> wrote:
>>>>>> 
>>>>>>> Hi,
>>>>>>> 
>>>>>>> "make check" runs ctest behind the scenes. You can get some more
>>>>>>> information by running ctest directly. From your build directory,
>>> try
>>>>>>> 
>>>>>>> ctest --output-on-failure --tests-regex "MdrunMpiTests"
>>>>>>> However, I suspect your issues may be already covered at
>>>>>>> http://manual.gromacs.org/documentation/2016/install-
>>>>>>> guide/index.html#testing-gromacs-for-correctness
>>>>>>> e.g.
>>>>>>> that you have done an MPI build, but you need to customize how you
>>>>> start
>>>>>>> your MPI enabled binaries.
>>>>>>> 
>>>>>>> Mark