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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical and Materials Physics, Chemical and Biomolecular Engineering, Biomedical Engineering, and Materials Science and Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Tue, May 7, 2024 at 8:57 AM Chakrabarti, Mayukh (NIH/NCI) [C] via AMBER < amber.ambermd.org> wrote: > Hello, > > I wanted to update my report below to mention that the issue with pbsa > binaries breaking upon enabling the LibTorch & cudnn libraries still > persists in Amber24 with AmberTools 24. I compiled with CUDA 10.2, gcc 8.5, > OpenMPI 4.1.5, python 3.10, and cmake 3.25.2 on a Red Hat Enterprise Linux > release 8.8 (Ootpa) system. I am not aware of any workaround or resolution > for this issue. > > Best, > > Mayukh Chakrabarti (he/him) > COMPUTATIONAL SCIENTIST > > From: Chakrabarti, Mayukh (NIH/NCI) [C] <mayukh.chakrabarti.nih.gov> > Date: Tuesday, October 31, 2023 at 11:28 AM > To: amber.ambermd.org <amber.ambermd.org> > Subject: Amber22/AmberTools23: Enabling of libtorch & cudnn libraries > breaks pbsa binaries > Hello, > > I am encountering a problem in which enabling LibTorch libraries with > Amber22 and AmberTools23 causes segmentation fault errors (SIGSEGV) in the > pbsa binaries upon running the serial tests (make test.serial). I have > successfully compiled a version of Amber22/AmberTools23 in which this > library is not enabled, and none of the pbsa tests in AmberTools break > (i.e., no segmentation fault errors). > > Further details: > > I am running my compilation with CUDA 10.2, gcc 8.5, OpenMPI 4.1.5, python > 3.6, and cmake 3.25.1 on a Red Hat Enterprise Linux release 8.8 (Ootpa) > system. As per the manual, I have tried both “Built-in” mode and > “User-installed” mode, both resulting in the same errors. For the > “User-installed” mode, I manually downloaded and extracted > “libtorch-shared-with-deps-1.9.1+cu102.zip” from the PyTorch website to > correspond to CUDA 10.2, and > “cudnn-linux-x86_64-8.7.0.84_cuda10-archive.tar.xz” directly from the > NVIDIA website, and specified the following variables to CMAKE: > > > -DLIBTORCH=ON \ > > -DTORCH_HOME=/path_to_libtorch \ > > -DCUDNN=TRUE \ > > -DCAFFE2_USE_CUDNN=1 \ > > -DCUDNN_INCLUDE_PATH=/path_to_cudnn_include \ > > -DCUDNN_LIBRARY_PATH=/path_to_libcudnn.so \ > > > Building and compiling proceed without issue. However, when running the > serial tests, I get errors akin to the following (example shown after > sourcing amber.sh and running AmberTools pbsa_ligand test): > > Program received signal SIGSEGV: Segmentation fault - invalid memory > reference. > > Backtrace for this error: > #0 0x7f480cb65171 in ??? > #1 0x7f480cb64313 in ??? > #2 0x7f480c221c0f in ??? > #3 0x7f4869667219 in ??? > #4 0x7f480c224856 in ??? > #5 0x7f4869648722 in ??? > ./Run.t4bnz.min: line 34: 2436022 Segmentation fault (core dumped) > $DO_PARALLEL $TESTpbsa -O -i min.in -o $output < /dev/null > ./Run.t4bnz.min: Program error > > When running the exact same test with the version of Amber22 not > containing the LibTorch libraries: > > diffing mdout.lig.min.save with mdout.lig.min > PASSED > ============================================================== > > I have run ‘ldd’ on the pbsa binary to try to identify any libraries that > may be missing, but there don’t appear to be any missing libraries. Could > anybody please provide any insight into how to fix this issue? > > Best, > > Mayukh Chakrabarti > COMPUTATIONAL SCIENTIST > > > > > > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!PLN2_ZzXkAP-XJnmppjnXaq9ruj3FNFdRR163QR8ehrjX6YYBOUfKc8Eo0t0w7N8I3CtOwXatyYNzg$ > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed May 08 2024 - 10:30:03 PDT