# Hello all. I have following error. please help I m new to gromacs **URL:** \ **Category:** User discussions\ **Created:** [March 8, 2024, 1:48am UTC](https://gromacs.bioexcel.eu/t/hello-all-i-have-following-error-please-help-i-m-new-to-gromacs/8552 "2024-03-08T01:48:38Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Anandsingpatil1983](https://avatars.discourse-cdn.com/v4/letter/a/ccd318/32.png) [@Anandsingpatil1983](https://gromacs.bioexcel.eu/u/Anandsingpatil1983)\ **Post date:** [March 8, 2024, 1:48am UTC](https://gromacs.bioexcel.eu/t/hello-all-i-have-following-error-please-help-i-m-new-to-gromacs/8552/1 "2024-03-08T01:48:38Z")
GROMACS version: GROMACS modification: Yes/No Here post your question :-) GROMACS - gmx pdb2gmx, 2020.1-Ubuntu-2020.1-1 (-: ``` GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd ``` Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf Artem Zhmurov and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2019, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out [http://www.gromacs.org](http://www.gromacs.org) for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/anand/Desktop/Kiranmd1 Command line: gmx pdb2gmx -f 4jkv\_clean.pdb -o 4jkv\_processed.gro -water spce Select the Force Field: From current directory: 1: CHARMM all-atom force field From ‘/usr/share/gromacs/top’: 2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002) 9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 10: GROMOS96 43a1 force field 11: GROMOS96 43a2 force field (improved alkane dihedrals) 12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9) 16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 1 Using the Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff going to rename ./charmm36-jul2022.ff/aminoacids.r2b Opening force field file ./charmm36-jul2022.ff/aminoacids.r2b going to rename ./charmm36-jul2022.ff/carb.r2b Opening force field file ./charmm36-jul2022.ff/carb.r2b going to rename ./charmm36-jul2022.ff/cgenff.r2b Opening force field file ./charmm36-jul2022.ff/cgenff.r2b going to rename ./charmm36-jul2022.ff/ethers.r2b Opening force field file ./charmm36-jul2022.ff/ethers.r2b going to rename ./charmm36-jul2022.ff/lipid.r2b Opening force field file ./charmm36-jul2022.ff/lipid.r2b going to rename ./charmm36-jul2022.ff/metals.r2b Opening force field file ./charmm36-jul2022.ff/metals.r2b going to rename ./charmm36-jul2022.ff/na.r2b Opening force field file ./charmm36-jul2022.ff/na.r2b going to rename ./charmm36-jul2022.ff/silicates.r2b Opening force field file ./charmm36-jul2022.ff/silicates.r2b going to rename ./charmm36-jul2022.ff/solvent.r2b Opening force field file ./charmm36-jul2022.ff/solvent.r2b Reading 4jkv\_clean.pdb… WARNING: all CONECT records are ignored Read ‘SOLUBLE CYTOCHROME B562, SMOOTHENED HOMOLOG’, 3532 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 454 residues with 3532 atoms chain #res #atoms 1 ‘A’ 454 3532 All occupancies are one Opening force field file ./charmm36-jul2022.ff/atomtypes.atp Reading residue database… (Charmm36-jul2022) Opening force field file ./charmm36-jul2022.ff/aminoacids.rtp Opening force field file ./charmm36-jul2022.ff/carb.rtp Opening force field file ./charmm36-jul2022.ff/cgenff.rtp Opening force field file ./charmm36-jul2022.ff/ethers.rtp Opening force field file ./charmm36-jul2022.ff/lipid.rtp Opening force field file ./charmm36-jul2022.ff/metals.rtp Opening force field file ./charmm36-jul2022.ff/na.rtp Opening force field file ./charmm36-jul2022.ff/silicates.rtp Opening force field file ./charmm36-jul2022.ff/solvent.rtp Opening force field file ./charmm36-jul2022.ff/aminoacids.hdb Opening force field file ./charmm36-jul2022.ff/carb.hdb Opening force field file ./charmm36-jul2022.ff/cgenff.hdb Opening force field file ./charmm36-jul2022.ff/ethers.hdb Opening force field file ./charmm36-jul2022.ff/lipid.hdb Opening force field file ./charmm36-jul2022.ff/metals.hdb Opening force field file ./charmm36-jul2022.ff/na.hdb Opening force field file ./charmm36-jul2022.ff/silicates.hdb Opening force field file ./charmm36-jul2022.ff/solvent.hdb Opening force field file ./charmm36-jul2022.ff/aminoacids.n.tdb Opening force field file ./charmm36-jul2022.ff/carb.n.tdb Opening force field file ./charmm36-jul2022.ff/cgenff.n.tdb Opening force field file ./charmm36-jul2022.ff/ethers.n.tdb Opening force field file ./charmm36-jul2022.ff/lipid.n.tdb Opening force field file ./charmm36-jul2022.ff/metals.n.tdb Opening force field file ./charmm36-jul2022.ff/na.n.tdb Opening force field file ./charmm36-jul2022.ff/silicates.n.tdb Opening force field file ./charmm36-jul2022.ff/solvent.n.tdb Opening force field file ./charmm36-jul2022.ff/aminoacids.c.tdb Opening force field file ./charmm36-jul2022.ff/carb.c.tdb Opening force field file ./charmm36-jul2022.ff/cgenff.c.tdb Opening force field file ./charmm36-jul2022.ff/ethers.c.tdb Opening force field file ./charmm36-jul2022.ff/lipid.c.tdb Opening force field file ./charmm36-jul2022.ff/metals.c.tdb Opening force field file ./charmm36-jul2022.ff/na.c.tdb Opening force field file ./charmm36-jul2022.ff/silicates.c.tdb Opening force field file ./charmm36-jul2022.ff/solvent.c.tdb Processing chain 1 ‘A’ (3532 atoms, 454 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 646 donors and 635 acceptors were found. There are 842 hydrogen bonds Will use HISE for residue 63 Will use HISH for residue 227 Will use HISE for residue 231 Will use HISE for residue 340 Will use HISE for residue 361 Will use HISE for residue 433 Will use HISE for residue 470 Identified residue GLY-1 as a starting terminus. Identified residue CYS550 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: MET33 MET58 HIS63 CYS193 CYS213 CYS217 HIS227 SD262 SD447 NE2497 SG855 SG1014 SG1041 NE21124 MET58 SD447 2.190 HIS63 NE2497 1.890 1.460 CYS193 SG855 1.995 1.990 2.165 CYS213 SG1014 2.167 2.163 2.341 0.204 CYS217 SG1041 2.376 2.255 1.466 1.571 1.641 HIS227 NE21124 2.954 2.148 1.588 1.963 2.024 0.826 MET230 SD1148 3.821 2.963 2.255 2.914 2.953 1.599 0.982 HIS231 NE21159 3.104 2.437 1.562 2.418 2.492 1.009 0.566 CYS244 SG1247 5.001 4.500 3.401 4.611 4.666 3.071 2.760 CYS273 SG1479 4.907 4.892 3.764 4.302 4.301 2.855 2.856 MET286 SD1584 3.119 3.312 1.927 3.196 3.290 1.708 1.940 CYS295 SG1648 2.257 2.250 1.347 1.645 1.730 0.203 0.948 MET301 SD1690 2.803 2.514 2.035 1.474 1.465 0.658 0.910 CYS314 SG1787 2.966 3.219 2.262 2.233 2.242 0.967 1.491 MET326 SD1887 4.717 4.614 3.717 3.718 3.674 2.497 2.495 HIS340 NE22006 7.100 6.805 5.903 6.099 6.047 4.856 4.667 HIS361 NE22153 5.720 5.906 4.715 5.219 5.209 3.820 3.898 CYS390 SG2362 3.005 3.136 2.165 2.268 2.285 0.894 1.334 MET424 SD2632 7.360 6.857 6.092 6.200 6.138 5.037 4.746 HIS433 NE22706 8.286 7.967 6.990 7.433 7.395 6.095 5.874 MET449 SD2817 6.930 6.613 5.585 6.192 6.177 4.775 4.556 CYS469 SG2975 4.813 3.980 3.399 3.603 3.581 2.454 1.940 HIS470 NE22985 4.529 4.053 3.303 3.400 3.369 2.171 1.908 CYS490 SG3172 3.440 2.390 2.952 1.561 1.482 2.247 2.055 CYS507 SG3197 3.621 2.499 3.057 1.751 1.671 2.338 2.085 MET525 SD3339 4.462 4.053 3.086 3.672 3.683 2.219 1.976 MET532 SD3386 5.627 5.201 4.201 4.893 4.896 3.441 3.169 CYS550 SG3532 5.990 6.128 4.758 6.280 6.363 4.744 4.746 MET230 HIS231 CYS244 CYS273 MET286 CYS295 MET301 SD1148 NE21159 SG1247 SG1479 SD1584 SG1648 SD1690 HIS231 NE21159 0.733 CYS244 SG1247 1.923 2.250 CYS273 SG1479 2.240 2.487 1.635 MET286 SD1584 1.892 1.475 2.025 2.100 CYS295 SG1648 1.682 1.043 3.054 2.863 1.575 MET301 SD1690 1.619 1.285 3.276 2.895 2.214 0.854 CYS314 SG1787 1.780 1.442 2.819 2.135 1.547 0.983 1.066 MET326 SD1887 2.033 2.328 2.338 1.073 2.459 2.572 2.302 HIS340 NE22006 3.890 4.420 3.185 2.350 4.417 4.926 4.658 HIS361 NE22153 3.294 3.527 2.337 1.058 2.912 3.813 3.858 CYS390 SG2362 1.582 1.249 2.652 2.063 1.439 0.915 1.024 MET424 SD2632 3.946 4.554 3.447 2.816 4.782 5.132 4.772 HIS433 NE22706 5.015 5.555 3.872 3.395 5.390 6.144 5.971 MET449 SD2817 3.690 4.191 2.455 2.075 3.981 4.809 4.725 CYS469 SG2975 1.175 1.848 2.109 2.038 2.738 2.579 2.204 HIS470 NE22985 1.312 1.780 2.096 1.502 2.375 2.279 1.935 CYS490 SG3172 2.763 2.619 4.679 4.506 3.892 2.418 1.810 CYS507 SG3197 2.734 2.643 4.652 4.496 3.954 2.515 1.881 MET525 SD3339 1.214 1.622 1.332 1.060 1.843 2.264 2.222 MET532 SD3386 2.290 2.787 1.264 1.129 2.740 3.476 3.432 CYS550 SG3532 4.158 4.188 2.444 3.002 3.092 4.640 5.131 CYS314 MET326 HIS340 HIS361 CYS390 MET424 HIS433 SG1787 SD1887 NE22006 NE22153 SG2362 SD2632 NE22706 MET326 SD1887 1.756 HIS340 NE22006 4.164 2.432 HIS361 NE22153 3.003 1.817 2.045 CYS390 SG2362 0.206 1.716 4.107 2.974 MET424 SD2632 4.442 2.713 0.776 2.724 4.369 HIS433 NE22706 5.420 3.760 1.442 2.842 5.350 1.701 MET449 SD2817 4.147 2.621 1.156 1.742 4.057 1.633 1.436 CYS469 SG2975 2.295 1.571 2.978 2.970 2.144 2.900 4.178 HIS470 NE22985 1.748 0.861 2.788 2.447 1.630 2.878 4.076 CYS490 SG3172 2.866 3.749 5.841 5.483 2.832 5.744 7.187 CYS507 SG3197 2.935 3.728 5.766 5.476 2.892 5.645 7.107 MET525 SD3339 1.800 1.138 2.828 2.097 1.648 3.041 3.943 MET532 SD3386 2.937 1.681 1.935 1.629 2.811 2.217 2.806 CYS550 SG3532 4.338 4.057 4.378 2.902 4.243 4.919 4.490 MET449 CYS469 HIS470 CYS490 CYS507 MET525 MET532 SD2817 SG2975 NE22985 SG3172 SG3197 SD3339 SD3386 CYS469 SG2975 3.015 HIS470 NE22985 2.877 0.750 CYS490 SG3172 6.056 3.126 3.199 CYS507 SG3197 5.993 3.042 3.153 0.203 MET525 SD3339 2.593 1.140 0.807 3.674 3.647 MET532 SD3386 1.415 1.799 1.676 4.791 4.739 1.228 CYS550 SG3532 3.365 4.463 4.223 6.776 6.792 3.445 3.065 Linking CYS-193 SG-855 and CYS-213 SG-1014… Linking CYS-217 SG-1041 and CYS-295 SG-1648… Linking CYS-314 SG-1787 and CYS-390 SG-2362… Linking CYS-490 SG-3172 and CYS-507 SG-3197… Start terminus GLY–1: GLY-NH3+ End terminus CYS-550: COO- Opening force field file ./charmm36-jul2022.ff/aminoacids.arn Checking for duplicate atoms… Generating any missing hydrogen atoms and/or adding termini. * * * Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1 Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 130) Fatal error: Residue 7 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. For more information and tips for troubleshooting, please check the GROMACS website at [Common Errors — GROMACS webpage https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors) ---
**Author:** ![shataisheng](https://avatars.discourse-cdn.com/v4/letter/s/a9adbd/32.png) [@shataisheng](https://gromacs.bioexcel.eu/u/shataisheng)\ **Post date:** [March 8, 2024, 4:05am UTC](https://gromacs.bioexcel.eu/t/hello-all-i-have-following-error-please-help-i-m-new-to-gromacs/8552/2 "2024-03-08T04:05:56Z")
atom should be fixed，u can try swiss-pdb viewer software ---
**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\ **Post date:** [March 8, 2024, 6:02pm UTC](https://gromacs.bioexcel.eu/t/hello-all-i-have-following-error-please-help-i-m-new-to-gromacs/8552/3 "2024-03-08T18:02:11Z")
The error is saying your pdb file has atoms missing from the aspartic acid residue. You can search up tools online for fixing pdb files, such as this automated server for repairing protein pdb files ([https://pubs.acs.org/doi/10.1021/acs.jcim.2c00571](https://pubs.acs.org/doi/10.1021/acs.jcim.2c00571)) ---
**Author:** ![scinikhil](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/scinikhil/32/3483_2.png) [@scinikhil](https://gromacs.bioexcel.eu/u/scinikhil)\ **Post date:** [March 8, 2024, 6:15pm UTC](https://gromacs.bioexcel.eu/t/hello-all-i-have-following-error-please-help-i-m-new-to-gromacs/8552/4 "2024-03-08T18:15:54Z")
> [@Anandsingpatil1983](#): > > Residue 7 named ASP of a molecule in the input file was mapped > to an entry in the topology database, but the atom CG used in > that entry is not found in the input file. Perhaps your atom > and/or residue naming needs to be fixed. search with this in google, you will find a lot of hits. ---
**Author:** ![Anandsingpatil1983](https://avatars.discourse-cdn.com/v4/letter/a/ccd318/32.png) [@Anandsingpatil1983](https://gromacs.bioexcel.eu/u/Anandsingpatil1983)\ **Post date:** [March 11, 2024, 12:42am UTC](https://gromacs.bioexcel.eu/t/hello-all-i-have-following-error-please-help-i-m-new-to-gromacs/8552/5 "2024-03-11T00:42:44Z")
Thanks Error fixed. ---
**Author:** ![Anandsingpatil1983](https://avatars.discourse-cdn.com/v4/letter/a/ccd318/32.png) [@Anandsingpatil1983](https://gromacs.bioexcel.eu/u/Anandsingpatil1983)\ **Post date:** [March 11, 2024, 12:43am UTC](https://gromacs.bioexcel.eu/t/hello-all-i-have-following-error-please-help-i-m-new-to-gromacs/8552/6 "2024-03-11T00:43:47Z")
Thanks error fixed. ---
**Author:** ![Anandsingpatil1983](https://avatars.discourse-cdn.com/v4/letter/a/ccd318/32.png) [@Anandsingpatil1983](https://gromacs.bioexcel.eu/u/Anandsingpatil1983)\ **Post date:** [March 29, 2024, 6:41pm UTC](https://gromacs.bioexcel.eu/t/hello-all-i-have-following-error-please-help-i-m-new-to-gromacs/8552/7 "2024-03-29T18:41:42Z")
anand@anand:~/Downloads/12/gromacs-2024.1/build$ cmake … -DGMX\_GPU=CUDA -DCUDA\_TOOLKIT\_ROOT\_DIR=/usr/local/cuda – The C compiler identification is GNU 9.4.0 – The CXX compiler identification is GNU 9.4.0 – Detecting C compiler ABI info – Detecting C compiler ABI info - done – Check for working C compiler: /usr/bin/cc - skipped – Detecting C compile features – Detecting C compile features - done – Detecting CXX compiler ABI info – Detecting CXX compiler ABI info - done – Check for working CXX compiler: /usr/bin/c++ - skipped – Detecting CXX compile features – Detecting CXX compile features - done – Found Python3: /usr/bin/python3.8 (found suitable version “3.8.10”, minimum required is “3.7”) found components: Interpreter Development Development.Module Development.Embed – Selected GPU FFT library - cuFFT – Found OpenMP\_C: -fopenmp (found version “4.5”) – Found OpenMP\_CXX: -fopenmp (found version “4.5”) – Found OpenMP: TRUE (found version “4.5”) – Performing Test CFLAGS\_WARN\_NO\_MISSING\_FIELD\_INITIALIZERS – Performing Test CFLAGS\_WARN\_NO\_MISSING\_FIELD\_INITIALIZERS - Success – Performing Test CFLAGS\_EXCESS\_PREC – Performing Test CFLAGS\_EXCESS\_PREC - Success – Performing Test CFLAGS\_COPT – Performing Test CFLAGS\_COPT - Success – Performing Test CFLAGS\_NOINLINE – Performing Test CFLAGS\_NOINLINE - Success – Performing Test CXXFLAGS\_WARN\_NO\_MISSING\_FIELD\_INITIALIZERS – Performing Test CXXFLAGS\_WARN\_NO\_MISSING\_FIELD\_INITIALIZERS - Success – Performing Test CXXFLAGS\_EXCESS\_PREC – Performing Test CXXFLAGS\_EXCESS\_PREC - Success – Performing Test CXXFLAGS\_COPT – Performing Test CXXFLAGS\_COPT - Success – Performing Test CXXFLAGS\_NOINLINE – Performing Test CXXFLAGS\_NOINLINE - Success – Looking for include file unistd.h – Looking for include file unistd.h - found – Looking for include file pwd.h – Looking for include file pwd.h - found – Looking for include file dirent.h – Looking for include file dirent.h - found – Looking for include file time.h – Looking for include file time.h - found – Looking for include file sys/time.h – Looking for include file sys/time.h - found – Looking for include file io.h – Looking for include file io.h - not found – Looking for include file sched.h – Looking for include file sched.h - found – Looking for include file xmmintrin.h – Looking for include file xmmintrin.h - found – Looking for gettimeofday – Looking for gettimeofday - found – Looking for sysconf – Looking for sysconf - found – Looking for nice – Looking for nice - found – Looking for fsync – Looking for fsync - found – Looking for \_fileno – Looking for \_fileno - not found – Looking for fileno – Looking for fileno - found – Looking for \_commit – Looking for \_commit - not found – Looking for sigaction – Looking for sigaction - found – Performing Test HAVE\_BUILTIN\_CLZ – Performing Test HAVE\_BUILTIN\_CLZ - Success – Performing Test HAVE\_BUILTIN\_CLZLL – Performing Test HAVE\_BUILTIN\_CLZLL - Success – Looking for clock\_gettime in rt – Looking for clock\_gettime in rt - found – Looking for feenableexcept in m – Looking for feenableexcept in m - found – Looking for fedisableexcept in m – Looking for fedisableexcept in m - found – Checking for sched.h GNU affinity API – Performing Test sched\_affinity\_compile – Performing Test sched\_affinity\_compile - Success – Looking for include file mm\_malloc.h – Looking for include file mm\_malloc.h - found – Looking for include file malloc.h – Looking for include file malloc.h - found – Checking for \_mm\_malloc() – Checking for \_mm\_malloc() - supported – Looking for posix\_memalign – Looking for posix\_memalign - found – Looking for memalign – Looking for memalign - not found – Using default binary suffix: “” – Using default library suffix: “” – Performing Test CMAKE\_HAVE\_LIBC\_PTHREAD – Performing Test CMAKE\_HAVE\_LIBC\_PTHREAD - Failed – Looking for pthread\_create in pthreads – Looking for pthread\_create in pthreads - not found – Looking for pthread\_create in pthread – Looking for pthread\_create in pthread - found – Found Threads: TRUE – Looking for C++ include pthread.h – Looking for C++ include pthread.h - found – Performing Test TEST\_ATOMICS – Performing Test TEST\_ATOMICS - Success – Atomic operations found – Performing Test PTHREAD\_SETAFFINITY – Performing Test PTHREAD\_SETAFFINITY - Success – Detecting best SIMD instructions for this CPU – Checking for GCC x86 inline asm – Checking for GCC x86 inline asm - supported – Detected build CPU features - aes apic avx clfsh cmov cx8 cx16 htt intel lahf mmx msr nonstop\_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt – Detected build CPU brand - Intel(R) Core™ i5-2320 CPU @ 3.00GHz – Detected best SIMD instructions for this CPU - AVX\_256 – Performing Test C\_mavx\_FLAG\_ACCEPTED – Performing Test C\_mavx\_FLAG\_ACCEPTED - Success – Performing Test C\_mavx\_COMPILE\_WORKS – Performing Test C\_mavx\_COMPILE\_WORKS - Success – Performing Test CXX\_mavx\_FLAG\_ACCEPTED – Performing Test CXX\_mavx\_FLAG\_ACCEPTED - Success – Performing Test CXX\_mavx\_COMPILE\_WORKS – Performing Test CXX\_mavx\_COMPILE\_WORKS - Success – Enabling 256-bit AVX SIMD instructions using CXX flags: -mavx – Detecting flags to enable runtime detection of AVX-512 units on newer CPUs – Performing Test C\_xCORE\_AVX512\_qopt\_zmm\_usage\_high\_FLAG\_ACCEPTED – Performing Test C\_xCORE\_AVX512\_qopt\_zmm\_usage\_high\_FLAG\_ACCEPTED - Failed – Performing Test C\_xCORE\_AVX512\_FLAG\_ACCEPTED – Performing Test C\_xCORE\_AVX512\_FLAG\_ACCEPTED - Failed – Performing Test C\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_FLAG\_ACCEPTED – Performing Test C\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_FLAG\_ACCEPTED - Success – Performing Test C\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_COMPILE\_WORKS – Performing Test C\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_COMPILE\_WORKS - Success – Performing Test CXX\_xCORE\_AVX512\_qopt\_zmm\_usage\_high\_FLAG\_ACCEPTED – Performing Test CXX\_xCORE\_AVX512\_qopt\_zmm\_usage\_high\_FLAG\_ACCEPTED - Failed – Performing Test CXX\_xCORE\_AVX512\_FLAG\_ACCEPTED – Performing Test CXX\_xCORE\_AVX512\_FLAG\_ACCEPTED - Failed – Performing Test CXX\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_FLAG\_ACCEPTED – Performing Test CXX\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_FLAG\_ACCEPTED - Success – Performing Test CXX\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_COMPILE\_WORKS – Performing Test CXX\_mavx512f\_mfma\_mavx512vl\_mavx512dq\_mavx512bw\_COMPILE\_WORKS - Success – Detecting flags to enable runtime detection of AVX-512 units on newer CPUs - -mavx512f -mfma -mavx512vl -mavx512dq -mavx512bw – Performing Test \_Wno\_unused\_command\_line\_argument\_FLAG\_ACCEPTED – Performing Test \_Wno\_unused\_command\_line\_argument\_FLAG\_ACCEPTED - Success – Performing Test \_callconv\_\_\_vectorcall – Performing Test \_callconv\_\_\_vectorcall - Failed – Performing Test \_callconv\_\_\_regcall – Performing Test \_callconv\_\_\_regcall - Failed – Performing Test _callconv_ – Performing Test _callconv_ - Success – Found CUDA: /usr/local/cuda (found suitable version “12.4”, minimum required is “11.0”) – Adding work-around for issue compiling CUDA code with glibc 2.23 string.h – Check for working NVCC/C++ compiler combination with nvcc ‘/usr/local/cuda/bin/nvcc’ – Check for working NVCC/C++ compiler combination - works – Checking if nvcc accepts flags --generate-code=arch=compute\_35,code=sm\_35 – Checking if nvcc accepts flags --generate-code=arch=compute\_35,code=sm\_35 - No – Checking if nvcc accepts flags --generate-code=arch=compute\_37,code=sm\_37 – Checking if nvcc accepts flags --generate-code=arch=compute\_37,code=sm\_37 - No – Checking if nvcc accepts flags --generate-code=arch=compute\_50,code=sm\_50 – Checking if nvcc accepts flags --generate-code=arch=compute\_50,code=sm\_50 - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_52,code=sm\_52 – Checking if nvcc accepts flags --generate-code=arch=compute\_52,code=sm\_52 - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_60,code=sm\_60 – Checking if nvcc accepts flags --generate-code=arch=compute\_60,code=sm\_60 - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_61,code=sm\_61 – Checking if nvcc accepts flags --generate-code=arch=compute\_61,code=sm\_61 - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_70,code=sm\_70 – Checking if nvcc accepts flags --generate-code=arch=compute\_70,code=sm\_70 - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_75,code=sm\_75 – Checking if nvcc accepts flags --generate-code=arch=compute\_75,code=sm\_75 - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_80,code=sm\_80 – Checking if nvcc accepts flags --generate-code=arch=compute\_80,code=sm\_80 - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_86,code=sm\_86 – Checking if nvcc accepts flags --generate-code=arch=compute\_86,code=sm\_86 - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_89,code=sm\_89 – Checking if nvcc accepts flags --generate-code=arch=compute\_89,code=sm\_89 - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_90,code=sm\_90 – Checking if nvcc accepts flags --generate-code=arch=compute\_90,code=sm\_90 - Yes – Checking if nvcc accepts flags -Wno-deprecated-gpu-targets – Checking if nvcc accepts flags -Wno-deprecated-gpu-targets - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_53,code=sm\_53 – Checking if nvcc accepts flags --generate-code=arch=compute\_53,code=sm\_53 - Yes – Checking if nvcc accepts flags --generate-code=arch=compute\_80,code=sm\_80 – Checking if nvcc accepts flags --generate-code=arch=compute\_80,code=sm\_80 - Yes – Checking if nvcc accepts flags -use\_fast\_math – Checking if nvcc accepts flags -use\_fast\_math - Yes – Checking if nvcc accepts flags -Xptxas;-warn-double-usage – Checking if nvcc accepts flags -Xptxas;-warn-double-usage - Yes – Checking if nvcc accepts flags -Xptxas;-Werror – Checking if nvcc accepts flags -Xptxas;-Werror - Yes – The CUDA compiler identification is unknown CMake Error at /usr/local/share/cmake-3.28/Modules/CMakeDetermineCUDACompiler.cmake:270 (message): Failed to detect a default CUDA architecture. Compiler output: Call Stack (most recent call first): cmake/gmxManageCuda.cmake:116 (enable\_language) CMakeLists.txt:699 (include) – Configuring incomplete, errors occurred!