k-Wave

1. mcdannold
   

   Member
   Joined: Sep '15
   Posts: 5

   I tried running the gpu compiled code and am getting the following error:

   “./kspaceFirstOrder3D-CUDA: error while loading shared libraries: libmvec.so.1: cannot open shared object file: No such file or directory”

   I can't find this library, and my google searches are coming up empty. Does anyone have an idea where I might find it?

   I am also not sure I am doing this properly.

   Here is how I log into a node with a gpu:

   [njm7@login02 ~]$ srun -n 1 --pty -t 1:00:00 -p gpu --gres=gpu:1 bash
   srun: job 11701595 queued and waiting for resources
   srun: job 11701595 has been allocated resources
   [njm7@compute-g-16-175 ~]$ module load gcc/6.2.0
   [njm7@compute-g-16-175 ~]$ module load cuda/9.0
   [njm7@compute-g-16-175 ~]$ module load matlab/2017a
   [njm7@compute-g-16-175 ~]$ LD_PRELOAD='/n/app/gcc/6.2.0/lib64/libstdc++.so.6.0.22' matlab -nodesktop

   Here is what I get when I try to run the simulation using the compiled gpu binary:

   Running k-Wave simulation...
   start time: 05-Apr-2018 10:59:25
   reference sound speed: 3274.9813m/s
   dt: 7.6889ns, t_end: 119.708us, time steps: 15570
   input grid size: 44 by 44 by 492 grid points (14.5055 by 14.5055 by 162.1978mm)
   maximum supported frequency: 2.275MHz
   expanding computational grid...
   computational grid size: 64 by 64 by 512 grid points
   precomputation completed in 1.14s
   saving input files to disk...
   completed in 2.1249s
   system('export LD_LIBRARY_PATH=; cd /home/njm7/MFILES/k-Wave/binaries/; ./kspaceFirstOrder3D-CUDA -i /home/njm7/DATA/TMPat1Element0054a_105925.mat_input.h5 -o /home/njm7/DATA/TMPat1Element0054a_105925.mat_output.h5 --p_raw -s 14542' ,'-echo');
   ./kspaceFirstOrder3D-CUDA: error while loading shared libraries: libmvec.so.1: cannot open shared object file: No such file or directory

   Is this the right way to do this?

   Posted 6 years ago #

2. Jiri Jaros
   

   Developer
   Joined: Feb '12
   Posts: 115

   Hi
   I did see this problem on a couple of systems. libmvec is a C++ Math library with SSE/AVX vectorization, however, I'm not sure why the code cannot find it, it may have been replaced by Matlab. It also might be causes by the fact the code was compiled with GCC 5.4 and CUDA 8.0

   To solve it, I'd try one one of these possibilities:
   1. Try to run ./kspaceFirstOrder3D-CUDA to see what happens if the CUDA code is launched as a standalone application.
   1. Try to load proper modules.
   2. Find the libm.so file, typically it can be found in /lib/x86_64-linux-gnu and change the LD_LIBRARY_PATH in the system command.
   3. Try to download the libs from here: http://www.fit.vutbr.cz/~jarosjir/download/libm.tgz
   4. Recompile the code from sources. It should be easy, once you find the HDF5 module and set the paths to CUDA and HDF5 in the makefile.

   Best,
   Jiri

   Posted 6 years ago #

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