Hello,
I recently got ET working on my personal computer (virtual machine with ubuntu using the default ubuntu .cfg file), but I am having issues compiling the code on a local computer cluster using a custom .cfg file based off of the ubuntu .cfg (see end of email). However, when I attempt to compile the code on the cluster, it gets to the point where it begins building the executable, but then it prints out an error as seen below.
**Start Code Creating cactus_sim in /n/a3/srosofsky/Cactus/exe from [list of files]
/n/a3/srosofsky/Cactus/configs/sim/scratch/external/hwloc/lib/libhwloc.a(topolog\ y-linux.o): In function `hwloc_linux_set_area_membind': /n/a3/srosofsky/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src/topology\ -linux.c:1224: undefined reference to `mbind' /n/a3/srosofsky/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src/topology\ -linux.c:1243: undefined reference to `mbind' /n/a3/srosofsky/Cactus/configs/sim/scratch/external/hwloc/lib/libhwloc.a(topolog\ y-linux.o): In function `hwloc_linux_find_kernel_max_numnodes': /n/a3/srosofsky/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src/topology\ -linux.c:1347: undefined reference to `get_mempolicy' /n/a3/srosofsky/Cactus/configs/sim/scratch/external/hwloc/lib/libhwloc.a(topolog\ y-linux.o): In function `hwloc_linux_get_area_membind': /n/a3/srosofsky/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src/topology\ -linux.c:1445: undefined reference to `get_mempolicy' /n/a3/srosofsky/Cactus/configs/sim/scratch/external/hwloc/lib/libhwloc.a(topolog\ y-linux.o): In function `hwloc_linux_get_thisthread_membind': /n/a3/srosofsky/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src/topology\ -linux.c:1392: undefined reference to `get_mempolicy' /n/a3/srosofsky/Cactus/configs/sim/scratch/external/hwloc/lib/libhwloc.a(topolog\ y-linux.o): In function `hwloc_linux_set_thisthread_membind': /n/a3/srosofsky/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src/topology\ -linux.c:1291: undefined reference to `set_mempolicy' /n/a3/srosofsky/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src/topology\ -linux.c:1302: undefined reference to `migrate_pages' /n/a3/srosofsky/Cactus/configs/sim/scratch/build/hwloc/hwloc-1.10.1/src/topology\ -linux.c:1314: undefined reference to `set_mempolicy' collect2: ld returned 1 exit status make[1]: *** [/n/a3/srosofsky/Cactus/exe/cactus_sim] Error 1 make: *** [sim] Error 2 **End code
The above error occurs when the MPI_DIR in the .cfg file is set to /usr/lib64/openmpi/. I should note that when I change MPI_DIR to BUILD I get a different error message, but still at the same point in the compilation process.
**Start Code
Creating cactus_sim in /n/a3/srosofsky/Cactus/exe from [file list]
/usr/bin/ld: cannot find -lmpi_usempif08 collect2: ld returned 1 exit status make[1]: *** [/n/a3/srosofsky/Cactus/exe/cactus_sim] Error 1 make: *** [sim] Error 2
**End Code
Also, I looked at tickets 1717 and 1764 for possible overlap on this issue, but I had difficulty following how the issues in said tickets were resolved. Furthermore, the libnuma-dev and libltdl-dev libraries were installed but the problem still persists. I should note that I am currently using ET version ET_2015_11.
Any suggestions would be greatly appreciated.
Best, Shawn
Here is the configuration file that I used.
**Start Code
#MPI_DIR=BUILD
MPI_DIR = /usr/lib64/openmpi/
PTHREADS_DIR = NO_BUILD
HDF5_DIR = BUILD
HWLOC_DIR = BUILD
HWLOC_EXTRA_LIBS = hwloc
**End Code