[gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102

Nikolay Alemasov such3r at gmail.com
Thu Oct 17 04:42:52 CEST 2013 

Hello, Mark!

16.10.2013 18:17, Mark Abraham wrote:
> On Wed, Oct 16, 2013 at 12:27 PM, Nikolay Alemasov <such3r at gmail.com> wrote:
>
>> Thank you, Mark!
>>
>>      It was already tried. I mean a fresh unpacking and further cmake run.
>> As for your first thought concerning a loss of access to some parts of
>> gmxlib:
>>
>>> [alemasov at nks-g6 gromacs-4.6.3]$ ls -l ./src/gmxlib/ | grep -e "-" | cut
>>> -d' ' -f 1 | sort -n | uniq
>>> drwxr-x---
>>> -rw-r-----
>>>
>>      So there are only two permissions patterns which allow me to
>> read/write items in the directory. I am little bit confused. Are there any
>> limitations about OS or cmake versions? The latter is "cmake version
>> 2.8.12".
>>
> Also relevant are the owners, if you have unpacked as root and built as
> normal user, or vice-versa, etc. You should be doing nothing with root
> until you need to install, of course, and since you are installing to user
> space, you definitely should not be root.
     Checked it as well. Everything is done as a normal user as I am 
working on a computing cluster.
> CMake has not yet updated their compatibility matrix for 2.8.12 (
> http://www.cmake.org/Wiki/CMake_Version_Compatibility_Matrix/Commands) and
> as you can see there, things that used to work occasionally stop working.
> If you can try a different version of CMake we can rule out bugs in CMake
> 2.8.12.
     Configured the same way with cmake version 2.8.5. Fresh unpacked 
source used of course. The output is a bit different (note compiler 
identification mistake - should be Intel's - and fftw messages about SIMD):
> -- The C compiler identification is unknown
> -- Check for working C compiler: /usr/bin/gcc
> -- Check for working C compiler: /usr/bin/gcc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
...
> CMake Warning at CMakeLists.txt:962 (message):
>   The fftw library found is compiled without SIMD support, which makes it
>   slow.  Consider recompiling it or contact your admin
>
>
> -- Using external FFT library - FFTW3
> -- Using internal BLAS library
> -- LAPACK requires BLAS
> -- Using internal LAPACK library
> -- Checking for dlopen
> -- Performing Test HAVE_DLOPEN
> -- Performing Test HAVE_DLOPEN - Success
> -- Checking for dlopen - found
> -- Found the ability to use plug-ins when building shared libaries, so 
> will compile to use plug-ins (e.g. to read VMD-supported file formats).
> -- Checking for suitable VMD version
> -- VMD plugins not found. Path to VMD can be set with VMDDIR.
> CMake Error at src/gmxlib/CMakeLists.txt:102 (list):
>   list sub-command REMOVE_ITEM requires two or more arguments.
>
>
> CMake Error at src/gmxlib/CMakeLists.txt:105 (list):
>   list sub-command REMOVE_ITEM requires two or more arguments.
>
>
> You have called ADD_LIBRARY for library md without any source files. 
> This typically indicates a problem with your CMakeLists.txt file
> -- Configuring incomplete, errors occurred!
     So it seems that I have some problems with my file system or 
another system-kind failure. At least as that issue appears only for me.

P.S.

     Dear GROMACS users, please, can anybody share one's already 
compiled binary 4.6 version of x86_64, RedHat compatible built with CUDA?

Nikolay.

>
> Mark
>
>
>>   (Redirected from gmx-developers)
>>> The only way I can reproduce those symptoms is if I delete (or otherwise
>>> make unreadable) various parts of src/gmxlib. You may have deleted some
>>> files or been a different user at some point. I suggest you do a fresh
>>> unpack of the tarball and try again.
>>>
>>> Mark
>>>
>>>
>>> On Wed, Oct 16, 2013 at 7:19 AM, Nikolay Alemasov <such3r at gmail.com  <
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>>>
>>> wrote:
>>>
>>>> /  Greetings,
>>> />/
>>> />/      I am trying to compile the source code v.4.6.3 with cmake. The
>>> shell
>>> />/  script is (ran from the "build" directory inside gromacs source root
>>> dir):
>>> />/
>>> />/   CC=/ifs/opt/2013/intel/bin/icc
>>> />>/  CXX=/ifs/opt/2013/intel/bin/****icpc
>>> />>/  CMAKE_PREFIX_PATH="/ifs/home/****bionet/alemasov/libraries/****
>>> fftw"
>>> />>/
>>> />>/  cmake .. \
>>> />>/  -DGMX_GPU=OFF \
>>> />>/  -DGMX_CPU_ACCELERATION=SSE2 \
>>> />>/  -DFFTWF_LIBRARY='/ifs/home/****bionet/alemasov/libraries/****
>>> fftw/lib/libfftw3f.so'
>>> />>/  \
>>> />>/  -DFFTWF_INCLUDE_DIR='/ifs/****home/bionet/alemasov/****
>>> libraries/fftw/include'
>>> />>/  \
>>> />>/  -DCMAKE_INSTALL_PREFIX='/ifs/****home/bionet/alemasov/****
>>> libraries/gromacs'
>>> />>/
>>> />/
>>> />/  And get a message (successful part was cut):
>>> />/  ...
>>> />/
>>> />>/  -- Performing Test HAVE_DLOPEN
>>> />>/  -- Performing Test HAVE_DLOPEN - Success
>>> />>/  -- Checking for dlopen - found
>>> />>/  -- Found the ability to use plug-ins when building shared libaries,
>>> so
>>> />>/  will compile to use plug-ins (e.g. to read VMD-supported file
>>> formats).
>>> />>/  -- Checking for suitable VMD version
>>> />>/  -- VMD plugins not found. Path to VMD can be set with VMDDIR.
>>> />>/  CMake Error at src/gmxlib/CMakeLists.txt:102 (list):
>>> />>/    list sub-command REMOVE_ITEM requires two or more arguments.
>>> />>/
>>> />>/
>>> />>/  CMake Error at src/gmxlib/CMakeLists.txt:105 (list):
>>> />>/    list sub-command REMOVE_ITEM requires two or more arguments.
>>> />>/
>>> />>/
>>> />>/  You have called ADD_LIBRARY for library md without any source
>>> files. This
>>> />>/  typically indicates a problem with your CMakeLists.txt file
>>> />>/  -- Configuring incomplete, errors occurred!
>>> />>/  See also "/ifs/home/bionet/alemasov/****
>>> libraries/gromacs-4.6.3/build/****
>>> />>/  CMakeFiles/CMakeOutput.log".
>>> />>/  See also "/ifs/home/bionet/alemasov/****
>>> libraries/gromacs-4.6.3/build/****
>>> />>/  CMakeFiles/CMakeError.log".
>>> />>/
>>> />/
>>> />/  Below is a content of the src/gmxlib/CMakeLists.txt:99-****105:
>>> />/
>>> />>/  99 : # Files called xxx_test.c are test drivers with a main()
>>> function
>>> />>/  for module xxx.c,
>>> />>/  100: # so they should not be included in the library
>>> />>/  101: file(GLOB_RECURSE NOT_GMXLIB_SOURCES *_test.c *\#*)
>>> />>/  102: list(REMOVE_ITEM GMXLIB_SOURCES ${NOT_GMXLIB_SOURCES})
>>> />>/  103: # Selection has test_ instead of _test.
>>> />>/  104: file(GLOB SELECTION_TEST selection/test*)
>>> />>/  105: list(REMOVE_ITEM GMXLIB_SOURCES ${SELECTION_TEST})
>>> />>/
>>> />/
>>> />/  The target system:
>>> />/
>>> />/   Linux nks-g6.sscc.ru 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT
>>> 2009
>>> />>/  x86_64 x86_64 x86_64 GNU/Linux
>>> />>/  Red Hat Enterprise Linux Server release 5.4 (Tikanga)
>>> />>/  model name    : Intel(R) Xeon(R) CPU           X5560  @ 2.80GHz
>>> />>/
>>> />/
>>> />/  Please help me to sort out the issue. In fact my primary aim was to
>>> build
>>> />/  GPU-version of the GROMACS, but I can not do it even for the simplest
>>> />/  variant.
>>> />/  --
>>> />/  gmx-developers mailing list
>>> />/  gmx-developers at gromacs.org  <http://lists.gromacs.org/**
>>> mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> />/  http://lists.gromacs.org/****mailman/listinfo/gmx-****developers<http://lists.gromacs.org/**mailman/listinfo/gmx-**developers>
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>>> />
>>>
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