<div>Hi Ole,</div><div><br></div><div>I tried building the pdbg binary, but I came across "undefined reference" errors during compilation for libxsmm<br></div><div><br></div><div>/opt/chem/CP2K/cp2k-7.1.0/tools/build_utils/fypp -n --line-marker-format=gfortran5 /opt/chem/CP2K/cp2k-7.1.0/src/eri_mme/eri_mme_lattice_summation.F eri_mme_lattice_summation.F90<br>/opt/chem/CP2K/cp2k-7.1.0/tools/toolchain/install/libxsmm-1.14/lib/libxsmm.a(libxsmm_gemm.o): In function `__real_dgemm_':<br>libxsmm_gemm.c:(.text.__real_dgemm_+0x1): undefined reference to `dgemm_'<br>/opt/chem/CP2K/cp2k-7.1.0/tools/toolchain/install/libxsmm-1.14/lib/libxsmm.a(libxsmm_gemm.o): In function `__real_sgemm_':<br>libxsmm_gemm.c:(.text.__real_sgemm_+0x1): undefined reference to `sgemm_'<br>/opt/chem/CP2K/cp2k-7.1.0/tools/toolchain/install/libxsmm-1.14/lib/libxsmm.a(libxsmm_gemm.o): In function `__real_dgemv_':<br>libxsmm_gemm.c:(.text.__real_dgemv_+0x1): undefined reference to `dgemv_'<br>/opt/chem/CP2K/cp2k-7.1.0/tools/toolchain/install/libxsmm-1.14/lib/libxsmm.a(libxsmm_gemm.o): In function `__real_sgemv_':<br>libxsmm_gemm.c:(.text.__real_sgemv_+0x1): undefined reference to `sgemv_'<br>collect2: error: ld returned 1 exit status<br>/opt/chem/CP2K/cp2k-7.1.0/obj/local/pdbg/all.dep:108: recipe for target '/opt/chem/CP2K/cp2k-7.1.0/exe/local/graph.pdbg' failed<br>make[3]: *** [/opt/chem/CP2K/cp2k-7.1.0/exe/local/graph.pdbg] Error 1<br><br></div><div>I used the standard local.pdbg that was created by toolchain.</div><div>Is this some sort of linking error? Any idea how to resolve that?</div><div><br></div><div><br></div><div>Best wishes,</div><div>Paul<br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">Paul Schwarz schrieb am Dienstag, 11. August 2020 um 15:06:06 UTC+2:<br/></div><blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi Ole,<div><br></div><div>thanks for your reply.</div><div>I will try out the pdbg binary, and compare output to the known leaks.<br></div><div><br></div><div><br></div><div>Paul<br><br></div><div class="gmail_quote"><div dir="auto" class="gmail_attr">Ole Schütt schrieb am Dienstag, 11. August 2020 um 14:16:53 UTC+2:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Paul, <br> <br>you can run the pdbg binary which has LeakSanitizer enabled. When CP2K <br>exits it will print a detailed report of code locations that leaked <br>memory. <br> <br>Note that there are already a few known leaks which we usually ignore: <br> <br> <br><a href="https://github.com/cp2k/cp2k/blob/master/tools/toolchain/scripts/install_gcc.sh#L165" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=de&q=https://github.com/cp2k/cp2k/blob/master/tools/toolchain/scripts/install_gcc.sh%23L165&source=gmail&ust=1597306583293000&usg=AFQjCNEcOZV4kmrooiq5L3OYpRp7zVro1w">https://github.com/cp2k/cp2k/blob/master/tools/toolchain/scripts/install_gcc.sh#L165</a> <br> <br>Generally, those leaks are considered benign, but if nothing else show <br>up then you might want to check them as well. <br> <br>Cheers, <br>Ole <br> <br> <br>On 2020-08-11 13:54, Paul Schwarz wrote: <br>> Dear CP2K developers, <br>> <br>> I downloaded the latest 7.1 version and used toolchain to install the <br>> libraries libint, libxc, and libxsmm with the following command: <br>> <br>> $ ./install_cp2k_toolchain.sh --enable-omp --with-libxc=install <br>> --with-libint=install --with-fftw=system --with-libxsmm=install <br>> --with-mkl=system --with-elpa=no --with-cmake=system <br>> --with-openblas=no --with-hdf5=system <br>> <br>> After the successfull installations, I used the resulting local.popt <br>> to make an executable (without any further modifications). <br>> <br>> The used compilers were gcc, g++, and mpif90, which in my case is <br>> Intel version 2019.5.281, and not OpenMPI. <br>> <br>> Running relaxation simulations of molecules on slab surfaces, I <br>> experience an increasing memory usage. <br>> <br>> Sometimes the simulation relaxes fast enough, so that I don’t run <br>> out of memory. <br>> <br>> Sometimes I run out of memory before the relaxation finishes. <br>> <br>> I call cp2k_shell.popt, since I run my relaxations via an ase <br>> interface (but I guess it doesn’t matter, since there is no shell <br>> binary, but just a link of the shell to cp2k.popt). <br>> <br>> Does anyone else experience memory issues? I have the same issue on a <br>> HPC center, where a system admin installed the 7.1 version for me, and <br>> here my jobs also crash due to running out of memory. <br>> <br>> Does someone have a suggestion as to what the problem is or how to <br>> avoid it? <br>> <br>> Is there maybe a compiler flag/option I should avoid or put in? <br>> <br>> Best regards, <br>> <br>> Paul Schwarz <br>> <br>> -- <br>> You received this message because you are subscribed to the Google <br>> Groups "cp2k" group. <br>> To unsubscribe from this group and stop receiving emails from it, send <br>> an email to <a rel="nofollow">cp...@googlegroups.com</a>. <br>> To view this discussion on the web visit <br>> <a href="https://groups.google.com/d/msgid/cp2k/d9628406-6b9d-4e00-8b6b-edfe1b765d54n%40googlegroups.com" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=de&q=https://groups.google.com/d/msgid/cp2k/d9628406-6b9d-4e00-8b6b-edfe1b765d54n%2540googlegroups.com&source=gmail&ust=1597306583294000&usg=AFQjCNG3LoQYWPBOJJdBzX060WJDuv8Y0g">https://groups.google.com/d/msgid/cp2k/d9628406-6b9d-4e00-8b6b-edfe1b765d54n%40googlegroups.com</a> <br>> [1]. <br>> <br>> <br>> Links: <br>> ------ <br>> [1] <br>> <a href="https://groups.google.com/d/msgid/cp2k/d9628406-6b9d-4e00-8b6b-edfe1b765d54n%40googlegroups.com?utm_medium=email&utm_source=footer" rel="nofollow" target="_blank" data-saferedirecturl="https://www.google.com/url?hl=de&q=https://groups.google.com/d/msgid/cp2k/d9628406-6b9d-4e00-8b6b-edfe1b765d54n%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1597306583294000&usg=AFQjCNF6FUcNwxT4w092c7CQyASGJcdMtw">https://groups.google.com/d/msgid/cp2k/d9628406-6b9d-4e00-8b6b-edfe1b765d54n%40googlegroups.com?utm_medium=email&utm_source=footer</a> <br></blockquote></div></blockquote></div>