ABySS/2.0.2-intel-2018a

moravveji commented 6 years ago

May I kindly ask for an easyconfig to install ABySS/2.0.2-intel-2018a? There is already an .eb file for the foss/2018a toolchain, but the intel one is missing. I tried to simply adapt from the existing .eb file with the foss/2018a, and somewhere down the build process, I get the following error message:

icpc -DHAVE_CONFIG_H -I. -I..  -I.. -I/data/leuven/sys/x0090231/easybuild/work/ABySS/abyss -isystem/apps/leuven/skylake/2018a/software/Boost/1.66.0-intel-2018a -isystem/apps/leuven/skylake/2018a/software/Boost/1.66.0-intel-2018a/include    -I/apps/leuven/skylake/2018a/software/sparsehash/2.0.3-GCCcore-6.4.0 -isystem/data/leuven/sys/x0090231/easybuild/work/ABySS/abyss/boost_1_56_0 -Wall -Wextra -g -O2 -MT ABYSS-abyss.o -MD -MP -MF .deps/ABYSS-abyss.Tpo -c -o ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc
In file included from ../Assembly/AssemblyAlgorithms.h(4),
                 from abyss.cc(7):
../Assembly/BranchGroup.h(215): error: no instance of overloaded function "std::swap" matches the specified type
        inline void swap(BranchGroup&, BranchGroup&) NOEXCEPT { assert(false); }
                    ^

compilation aborted for abyss.cc (code 2)
make[2]: *** [ABYSS-abyss.o] Error 2
make[2]: Leaving directory `/vsc-hard-mounts/leuven-data/sys/x0090231/easybuild/work/ABySS/abyss/ABYSS'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/vsc-hard-mounts/leuven-data/sys/x0090231/easybuild/work/ABySS/abyss'
make: *** [all] Error 2

Building from the source also spits out the same curse. So, I am wondering if you could help me with a possible fix.

Thanks Ehsan.

ocaisa commented 6 years ago

If you can't get it to build manually either then you either need a patch or some special compiler flags. The best place to figure that out is from the ABySS developers. If you know what you need I can help at that point (but I have no experience with ABySS itself). But on another note...why stick with version 2.0.2? There have been two releases since then, 2.1.0 is the latest but requires some additional deps. 2.0.3 was a bugfix release in March and I think the simplest route is to try that since it is less likely to suffer from this problem.

boegel commented 6 years ago

@moravveji Any luck with getting ABySS 2.0.2 built with intel/2018a?

easybuilders / easybuild-easyconfigs

ABySS/2.0.2-intel-2018a #6603