Hello Lumir, Actually, we are not getting compilation errors when building GROMACS itself. It only fails in the testing phase. But when we do this step manually, after having loaded the necessary modules, it works fine. So that gives us the impression that it’s an EasyBuild issue instead…
— Franky > Op 20 okt. 2015, om 13:55 heeft Lumír Jasiok <[email protected]> het > volgende geschreven: > > Hi, > > did you received std::vector<double> constructor related errors? > > We had problem with intel/2015b toolchain and Gromacs as well. Problem is > probably caused by combination of ICC and GCC headers, please see > > https://software.intel.com/en-us/forums/intel-c-compiler/topic/565143 > > and > > Core Issue 1588 > (http://www.open-std.org/JTC1/SC22/WG21/docs/cwg_defects.html#1558) > > > Workaround would be using ictce/7.3.5 toolchain instead of intel/2015b. It > works for us. > > Also you can use foss toolchain, but not with GCC 5.x. We were unable to > successfully build Gromacs with new GCC, only with GCC 4.9.x. > > S pozdravem / Best Regards > > Lumír Jasiok > > -- > > Bc. Lumír Jasiok > Junior HPC systems manager > > IIT4Innovations national supercomputing center > VŠB – Technical University of Ostrava > 17. listopadu 15/2172 | 708 33 Ostrava-Poruba | Czech Repulic > > e-mail: [email protected] | web: www.it4i.cz | telefon: +420 597 329 519 > > > > >> On 20 Oct 2015, at 13:37, Backeljauw Franky >> <[email protected]> wrote: >> >> Hello all, >> >> We are trying to install GROMACS 5.1 using intel/2015b. All goes fine, >> until testing begins; then we get several failures. >> However, running "ctest --output-on-failure" on command line after the >> intel/2015b has been loaded, says all tests have passed. >> >> We get the impression that only part of the environment is passed to the sub >> shells executing the tests. >> >> When we add “runtest = False” in the easyconfig file, all is fine again. >> Any idea how to avoid writing "runtest = False" in the .eb file? >> >> Here’s the easyconfig file: >> >> </begin easyconfig-file> >> name = 'GROMACS' >> version = "5.1" >> versionsuffix = '-hybrid' >> >> homepage = 'http://www.gromacs.org' >> description = """GROMACS is a versatile package to perform molecular >> dynamics, >> i.e. simulate the Newtonian equations of motion for systems with hundreds to >> millions of particles.""" >> >> toolchain = {'name': 'intel', 'version': '2015b'} >> toolchainopts = {'openmp': True, 'usempi': True} >> >> # eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.4.tar.gz >> source_urls = [ >> 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources >> 'http://gerrit.gromacs.org/download/', # regression tests sources >> ] >> >> sources = [ >> SOURCELOWER_TAR_GZ, >> 'regressiontests-%(version)s.tar.gz', >> ] >> >> patches = [ >> 'gromacs-%(version)s_gmxManageMPI_cmake.patch', >> ] >> >> builddependencies = [('CMake', '3.3.2')] >> >> dependencies = [('Boost', '1.59.0', '-Python-2.7.10')] >> >> # running test command line with module loaded is fine, but not from within >> the EB environment >> # runtest = False >> >> moduleclass = ‘bio' >> </end easyconfig-file> >> >> — Many thanks for your reply, >> >> Franky >> >
