[gmx-users] Problem compiling Gromacs 5.1

Fri Aug 21 17:22:34 CEST 2015

On 8/21/15 11:18 AM, Atsutoshi Okabe wrote:
> Thanks, Mark.
> I inserted quotation in line 52 as Mark suggested.
> I tried cmake again and got the only error.
> Boost >= 1.44 not found. Using minimal internal version. This may cause trouble if you plan on compiling/linking other software that uses Boost against GROMACS.
>
> I don't know what the error means, but I did make and make install.
> After finished, I checked /bin directory. But almost all commands which we need to execute(i.g mdrun, trjconv...) were not generated.
> Actually, onlyI the following file were generated in bin directory.
> bin/
> bin/xplor2gmx.pl
> bin/GMXRC.bash
> bin/gmx-completion-gmx_mpi.bash
> bin/demux.pl
> bin/GMXRC.zsh
> bin/GMXRC
> bin/gmx-completion.bash
> bin/GMXRC.csh
> bin/gmx_mpi
>
> What causes this problem?
>

There is no problem.  This is the new convention - one binary, called gmx (in 
this case gmx_mpi since you compiled with MPI) and everything is a module of 
that binary:

gmx grompp ...
gmx mdrun ...
(etc)

-Justin

> 2015/08/20 21:44、Mark Abraham <mark.j.abraham at gmail.com> のメール：
>
>> Hi,
>>
>> You should change line 52 from what it is, to what I suggested - which
>> inserts quotation marks around one of the variable interpolations.
>>
>> Mark
>>
>> On Thu, Aug 20, 2015 at 2:43 PM 岡部篤俊 <atsutoshi0708 at gmail.com> wrote:
>>
>>> Thanks, Peter.
>>> But , I mean I don’t know what line I should change to from line 52 of
>>> cmake/FindPhinx.cmake to solve this error.
>>>
>>> Leucer
>>>
>>> 2015/08/20 16:02、Kroon, P.C. <p.c.kroon at rug.nl> のメール：
>>>
>>>> Just use your favourite text editor.
>>>>
>>>> Peter
>>>>
>>>> On Thu, Aug 20, 2015 at 3:10 AM, <atsutoshi0708 at gmail.com> wrote:
>>>>
>>>>> Line 52 of cmake/FindSphinx.cmake file is written below.
>>>>> string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
>>>>> SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
>>>>>
>>>>> Can you tell me how I can change the line?
>>>>>
>>>>> Bests,
>>>>> Leucer
>>>>>
>>>>>
>>>>> 2015/08/19 23:11、Mark Abraham <mark.j.abraham at gmail.com> のメッセージ:
>>>>>
>>>>>> Hi,
>>>>>>> On Wed, Aug 19, 2015 at 3:49 PM 岡部篤俊 <atsutoshi0708 at gmail.com> wrote:
>>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> I am unable to  compile Gromamcs 5.1 using the following cmake
>>> command.
>>>>>>> cmake .. -DGMX_FFT_LIBRARY=fftpack
>>>>>>> -DCMAKE_INSTALL_PREFIX=gromacs/gromacs-5.1 -DGMX_DOUBLE=off
>>>>>>> -DGMX_THREAD_MPI=off -DGMX_MPI=on -DGMX_CPU_ACCELERATION=SSE4.1
>>>>>>
>>>>>>
>>>>>> Unrelated, but you now need to use -DGMX_SIMD=SSE4.1 to have the same
>>>>>> effect.
>>>>>>
>>>>>>
>>>>>>> -DGMX_USE_RDTSCP=off
>>>>>>>
>>>>>>> Then I got the error message.
>>>>>>> Boost >= 1.44 not found. Using minimal internal version. This may
>>> cause
>>>>>>> trouble if you plan on compiling/linking other software that uses
>>> Boost
>>>>>>> against GROMACS.
>>>>>>> CMake Error at cmake/FindSphinx.cmake:52 (string):
>>>>>>> string sub-command REGEX, mode REPLACE needs at least 6 arguments
>>> total
>>>>>>> to
>>>>>>> command.
>>>>>>> Call Stack (most recent call first):
>>>>>>> docs/CMakeLists.txt:62 (find_package)
>>>>>>>
>>>>>>> Could you advice what could be causing this error?
>>>>>>
>>>>>> We try to find Sphinx in case people want to build the new
>>> documentation,
>>>>>> but it looks like some part of the detection isn't reliable enough. Can
>>>>> you
>>>>>> please try changing line 52 of cmake/FindSphinx.cmake to read
>>>>>>
>>>>>>   string(REGEX REPLACE "Sphinx \\([^)]*\\) ([^ ]+)" "\\1"
>>>>>> SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
>>>>>>
>>>>>> and let us know how you go?
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>> I was able to compile Gromacs 5.0 using same cmake command….
>>>>>>>
>>>>>>> Bests,
>>>>>>> Leucer
>>>>>>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================