Hi, In the past I compiled gmx 2016.4 on our old cluster and this worked as expected. Now I just compiled 2018.3 only to find that the resulting binary was unexpectedly slow ... On each node I have a multi-core architecture with 12 logical threads, but htop shows that gmx uses only one thread. Google-ing i found that the problem is probably due to gmx not properly detecting my hardware as described here: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-January/117830.html
So as suggested in the above post i tried to re-compile gmx with the flag -DGMX_HWLOC=ON (after installing hwloc-2.0.2 locally). "cmake" reports no problem, but when i do "make" compilation stops with errors that are obviously related to hwloc ... see below. any ideas on how to resolve this so that 2018 runs as expected would be highly appreciated! cheers, Michael compiling gmx 2018: prompt> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=OFF -DCMAKE_INSTALL_PREFIX=/home/micb/local/gromacs-2018.3-bin -DGMX_HWLOC=ON -DCMAKE_C_COMPILER=/home/micb/local/bin/gcc -DCMAKE_CXX_COMPILER=/home/micb/local/bin/g++ -DCMAKE_LIBRARY_PATH=/home/micb/local/lib:/home/micb/local/lib64 no complaints here prompt> make -j 4 ... [ 96%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp: In function ?int gmx::{anonymous}::parseHwLocNuma(hwloc_topology_t, gmx::HardwareTopology::Machine*)?: /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:354:64: error: ?struct hwloc_obj? has no member named ?memory? machine->numa.nodes[i].memory = hwlocNumaNodes[i]->memory.total_memory; ^ /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:378:101: error: ?hwloc_get_whole_distance_matrix_by_depth? was not declared in this scope const struct hwloc_distances_s * dist = hwloc_get_whole_distance_matrix_by_depth(topo, depth); ^ /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:381:54: error: ?const struct hwloc_distances_s? has no member named ?latency_base? machine->numa.baseLatency = dist->latency_base; ^ /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:382:54: error: ?const struct hwloc_distances_s? has no member named ?latency_max? machine->numa.maxRelativeLatency = dist->latency_max; ^ /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:389:65: error: ?const struct hwloc_distances_s? has no member named ?latency? machine->numa.relativeLatency[i][j] = dist->latency[i*dist->nbobjs+j]; ^ /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:407:65: error: ?struct hwloc_obj? has no member named ?memory? machine->numa.nodes[0].memory = hwlocMachine->memory.total_memory; ^ /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp: In function ?void gmx::{anonymous}::parseHwLoc(gmx::HardwareTopology::Machine*, gmx::HardwareTopology::SupportLevel*, bool*)?: /home/micb/local/gromacs-2018.3/src/gromacs/hardware/hardwaretopology.cpp:507:36: error: ?HWLOC_TOPOLOGY_FLAG_IO_DEVICES? was not declared in this scope hwloc_topology_set_flags(topo, HWLOC_TOPOLOGY_FLAG_IO_DEVICES); ^ [ 96%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.