Hello, Mark!
16.10.2013 18:17, Mark Abraham wrote:
On Wed, Oct 16, 2013 at 12:27 PM, Nikolay Alemasov <suc...@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@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/**
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