Hello there!
I'm trying to compile gromacs 4.0.7 with icc, mkl and openmpi. The problem is that, when I set the environment to LDFLAGS=-L/home/opt/intel/cmkl/10.2.5.035/lib/em64t/ -L/usr/lib CPPFLAGS=-I/home/opt/intel/cmkl/10.2.5.035/include/ and edit line 26576 of ./config to read LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core $LIBS" instead of LIBS="-lmkl $LIBS", I get the following errors in config.log: ===== START ===== configure:26570: checking for DftiComputeForward in -lmkl configure:26614: cc -o conftest -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -I/home/opt/intel/cmkl/10.2.5.035/include/ -L/home/opt/intel/cmkl/10.2.5.035/lib/em64t/ -L/usr/lib conftest.c -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lm >&5 /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_ok_to_fork' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_single' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_ordered' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_thread_num' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_barrier' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_num_threads' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_num_procs' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_reduce_nowait' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_critical' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_serialized_parallel' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_critical' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `ompc_set_nested' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_nested' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_fini_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_in_parallel' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_push_num_threads' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_reduce_nowait' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `omp_get_max_threads' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_init_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_serialized_parallel' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_flush' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_single' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_next_8' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_dispatch_init_4' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_global_thread_num' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_end_ordered' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_fork_call' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_atomic_fixed8_add' /home/opt/intel/cmkl/10.2.5.035/lib/em64t//libmkl_intel_thread.so: undefined reference to `__kmpc_for_static_fini' collect2: ld returned 1 exit status ===== END ===== All other setups of CPPFLAGS and LDFLAGS, also with -lmkl in ./configure give "mkl not found" sort of errors. This one seems to be the setup that got most far. Any ideas to solve this? I have mkl versions 11.1/072 and 10.2.5.035. Linking to each of them gives similar errors. Thanks in advance -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
