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

[Mark Abraham]

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.

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.

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>
>> <http://lists.**gromacs.org/mailman/listinfo/**gmx-developers<http://lists.gromacs.org/mailman/listinfo/gmx-developers> <
>> http://lists.gromacs.org/****mailman/listinfo/gmx-****
>> developers%3Chttp://lists.**gromacs.org/mailman/listinfo/**gmx-developers<http://lists.gromacs.org/**mailman/listinfo/gmx-**developers%3Chttp://lists.gromacs.org/mailman/listinfo/gmx-developers>
>> >>
>> />/  Please don't post (un)subscribe requests to the list. Use the www
>> />/  interface or send it to gmx-developers-request@**groma**cs.org<http://gromacs.org><gmx-developers-request
>> at gromacs.org  <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> >>
>> />/  .
>> />
>>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>