http://www.k-wave.org/forum/topic/chmod-cannot-access-%e2%80%98kspacefirstorder-omp%e2%80%99-no-such-file-or-directory Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 23:29:13 +0000 http://bbpress.org/?v=1.0.2 q http://www.k-wave.org/forum/search.php http://www.k-wave.org/forum/topic/chmod-cannot-access-%e2%80%98kspacefirstorder-omp%e2%80%99-no-such-file-or-directory#post-7518 Thu, 21 May 2020 20:29:21 +0000 Jiri Jaros 7518@http://www.k-wave.org/forum/ <p>Hi ZJIANG,</p> <p>As I understood, you try to execute k-Wave on a cluster. </p> <p>- How many cores does a node have? 200 seems to be a huge number. If you don't have a massive NUMA machine, you'd very likely to be limited to 16-64 threads.</p> <p>- If you submit a job using PBS you can specify everything using the qsub command</p> <p><code>qsub -l select=1:ncpus=16:ompthreads=16</code></p> <p>This, e.g., asks for one node with 16 cores, one thread per core. The -t parameter is not necessary. I'd also recommend you to display the OMP environment by<br /> <code>export OMP_DISPLAY_ENV=true</code></p> <p>- Could you post here the node specification and the job script?</p> <p>- Answering the previous question, you have to load a GCC module 7.3 or newer. </p> <p>Best<br /> Jiri </p> http://www.k-wave.org/forum/topic/chmod-cannot-access-%e2%80%98kspacefirstorder-omp%e2%80%99-no-such-file-or-directory#post-7475 Mon, 04 May 2020 11:03:59 +0000 ZJIANG 7475@http://www.k-wave.org/forum/ <p>Hi Vich,</p> <p>Thanks for helping. It appered to be a problem caused by our server.</p> <p>I have another question. While runing a job that requires large memory, I keep getting errors saying exceed cpu numbers. I used these lines:<br /> export OMP_PLACES={0}:200:1<br /> export OMP_PROC_BIND=true</p> <p>and added '-t 200' after OMP. Do I have to increase the cpu numbers or is there a way to limit the use of cpus?</p> <p>thanks,</p> <p>Zheng </p> http://www.k-wave.org/forum/topic/chmod-cannot-access-%e2%80%98kspacefirstorder-omp%e2%80%99-no-such-file-or-directory#post-7467 Fri, 01 May 2020 19:09:04 +0000 vich 7467@http://www.k-wave.org/forum/ <p>What do you get if you run the following?</p> <p><code>strings /lib64/libstdc++.so.6 | grep CXX</code></p> <p>Depending on your Linux distribution, you may have to update a package called <code>gcc</code>, <code>libstdc++</code>, or something like that. </p> http://www.k-wave.org/forum/topic/chmod-cannot-access-%e2%80%98kspacefirstorder-omp%e2%80%99-no-such-file-or-directory#post-7464 Fri, 01 May 2020 12:43:56 +0000 ZJIANG 7464@http://www.k-wave.org/forum/ <p>Hi Bradley,</p> <p>Thanks for replying. You're right, I was looking at the wrong folder. After fixing it, I got these:</p> <p>./kspaceFirstOrder-OMP: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by ./kspaceFirstOrder-OMP)<br /> ./kspaceFirstOrder-OMP: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by ./kspaceFirstOrder-OMP)<br /> ./kspaceFirstOrder-OMP: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by ./kspaceFirstOrder-OMP)</p> <p>What does it mean? Is it because of the matlab script?</p> <p>bests,</p> <p>Zheng </p> http://www.k-wave.org/forum/topic/chmod-cannot-access-%e2%80%98kspacefirstorder-omp%e2%80%99-no-such-file-or-directory#post-7450 Fri, 01 May 2020 08:16:22 +0000 Bradley Treeby 7450@http://www.k-wave.org/forum/ <p>Hi Zheng,</p> <p>Does $PBS_O_WORKDIR point to /k-Wave/binaries/ ? It sounds like you're in the wrong folder.</p> <p>Brad. </p> http://www.k-wave.org/forum/topic/chmod-cannot-access-%e2%80%98kspacefirstorder-omp%e2%80%99-no-such-file-or-directory#post-7448 Thu, 30 Apr 2020 15:54:16 +0000 ZJIANG 7448@http://www.k-wave.org/forum/ <p>Hi,</p> <p>I've put kspaceFirstOrder-OMP file into k-wave binaries floder and 'dir(getkWavePath('binaries'))' confirms it (on Linux). When I run the code, 'SaveToDisk' generate input h5 files succefully but I get the error'chmod: cannot access ‘./kspaceFirstOrder-OMP’: No such file or directory' all the time. Could you please help to find out what is going wrong?</p> <p>here is my code:</p> <p>module load matlab</p> <p>cd $PBS_O_WORKDIR<br /> chmod +x ./kspaceFirstOrder-OMP<br /> ./kspaceFirstOrder-OMP -i test3.h5 -o testout.h5</p> <p>thanks!</p> <p>Zheng </p>