Package Details: gromacs 2024.1-2

Git Clone URL: https://aur.archlinux.org/gromacs.git (read-only, click to copy)
Package Base: gromacs
Description: A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
Upstream URL: http://www.gromacs.org/
Keywords: chemistry science simulations
Licenses: LGPL
Submitter: xyproto
Maintainer: hseara (vedranmiletic)
Last Packager: vedranmiletic
Votes: 23
Popularity: 0.000178
First Submitted: 2011-12-14 17:03 (UTC)
Last Updated: 2024-05-06 19:04 (UTC)

Dependencies (13)

Required by (1)

Sources (1)

Latest Comments

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JBauer commented on 2023-10-23 12:21 (UTC)

Addendum: $CXXFLAGS also needs to be reset:

export CXXFLAGS="$CFLAGS"

JBauer commented on 2023-10-23 07:59 (UTC)

@dalima

I think you were lucky. I still got the same error when using CC=/opt/cuda/bin/gcc and CXX=/opt/bin/g++.

This isn't really surprising since those are actually just symlinks to /usr/bin/gcc-12 and /usr/bin/g++-12. Did you use makepkg or did you build the software by hand?

@hseara

The source of the problem seems to be in the default CFLAGS used by makepkg found in /etc/makepkg.conf. They are

CFLAGS="-march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions \
        -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security \
        -fstack-clash-protection -fcf-protection"

I was able to make the core dump go away by changing -D_FORTIFY_SOURCE=2 to -D_FORTIFY_SOURCE=1. The documentation for this macro says that level 2 introduces some run-time memory checks which might cause some otherwise well-behaved programs to fail; level 1 only does compile time checking.

I was able to get the package to build and run without the error by adding the following to the PKGBUILD just after the CC and CXX lines:

export CFLAGS="-mtune=native -O3 -pipe -fno-plt -fexceptions \
   -Wp,-D_FORTIFY_SOURCE=1 -Wformat -Werror=format-security \
   -fstack-clash-protection -fcf-protection"

(I dropped -march=x86-64 because the FFT library wouldn't compile properly with it. -mtune=native and -O3 resulted in a small performance boost during testing.)

dalima commented on 2023-09-07 19:23 (UTC)

@hseara

I had the exact same error you mentioned there. I got past it by specifying cuda's own version of gcc and g++ before using cmake: export CC=/opt/cuda/bin/gcc export CXX=/opt/cuda/bin/g++

Also i think there is a typo where -GMX_GPU should be -DGMX_GPU

I dont know if that fixes it on all computers, or i just got lucky? CUDA version 12.2.0-1

hseara commented on 2022-10-31 09:01 (UTC)

Details Description:

For quite some time now, when using gromacs with cuda in archlinux results in a core dump.

/usr/lib/gcc/x86_64-pc-linux-gnu/11.3.0/include/c++/bits/unique_ptr.h:407: typename std::add_lvalue_reference<_Tp>::type std::unique_ptr<_Tp, _Dp>::operator*() const [with _Tp = DeviceStream; _Dp = std::default_delete<DeviceStream>; typename std::add_lvalue_reference<_Tp>::type = DeviceStream&]: Assertion 'get() != pointer()' failed.
Aborted (core dumped)

If I install the package using spack the package runs without problems. This means that the problem is somehow in cuda/gcc11 in arch does anyone have a clue what is going on?

Additional info: * package version(s)

gromacs@2022.2 cuda: 11.8 (it also happened in previous 11.7 versions) gcc@11.3.0 * config and/or log files etc.

  • link to upstream bug report, if any N/A

Steps to reproduce:

$ gmx mdrun -v -deffnm step5_11
:-) GROMACS - gmx mdrun, 2022.3-dev (-:

Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/hector/test_gromacs
Command line:
gmx mdrun -v -deffnm step5_11

Reading file step5_11.tpr, VERSION 2022.2 (single precision)
Changing nstlist from 20 to 100, rlist from 1.224 to 1.346

1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Using 16 OpenMP threads

/usr/lib/gcc/x86_64-pc-linux-gnu/11.3.0/include/c++/bits/unique_ptr.h:407: typename std::add_lvalue_reference<_Tp>::type std::unique_ptr<_Tp, _Dp>::operator*() const [with _Tp = DeviceStream; _Dp = std::default_delete<DeviceStream>; typename std::add_lvalue_reference<_Tp>::type = DeviceStream&]: Assertion 'get() != pointer()' failed.
Aborted (core dumped)

vedranmiletic commented on 2022-01-31 11:19 (UTC)

Could you update to version 2021.5? On my machine, 2021.4 fails the GammaDistributionTest.Output test in double precision, 2021.5 passes all tests.

E3LDDfrK commented on 2020-03-24 08:27 (UTC) (edited on 2020-05-04 14:58 (UTC) by E3LDDfrK)

@gardotd426 What changes did you make? Did you check this https://bbs.archlinux.org/viewtopic.php?pid=1870450#p1870450 ? I think adding options=(!buildflags) to PKGBUILD is the easiest way to solve this.

I think some people ignore that sometime people install the gromacs package to analyze the data without actually running the simulation on their computers. (In the sense that I use my old laptop that doesn't support AVX2 to analyze/manipulate the trajectories. Pretty sure I'm not alone in this.)

gardotd426 commented on 2020-03-23 08:13 (UTC)

This fails to build, even after changing /etc/makepkg.conf as suggested below. /proc/cpuinfo shows that my cpu does support avx2...


In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_2.c:71,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_2.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_8.c:114,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_8.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_3.c:78,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_3.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_7.c:115,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_7.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_9.c:160,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_9.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_10.c:138,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_10.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_6.c:99,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_6.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_11.c:183,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_11.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_4.c:82,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_4.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_13.c:229,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_13.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_12.c:150,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_12.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"
  ^~~~~
In file included from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/n1f.h:21,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/../common/n1fv_5.c:98,
                 from /tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_5.c:3:
/tmp/makepkg/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/simd-support/simd-avx2.h:43:2: error: #error "compiling simd-avx2.h without avx2 support"
 #error "compiling simd-avx2.h without avx2 support"

cat /proc/cpuinfo:


 cat /proc/cpuinfo
processor   : 0
vendor_id   : AuthenticAMD
cpu family  : 23
model       : 8
model name  : AMD Ryzen 5 2600X Six-Core Processor
stepping    : 2
microcode   : 0x800820d
cpu MHz     : 3962.182
cache size  : 512 KB
physical id : 0
siblings    : 12
core id     : 0
cpu cores   : 6
apicid      : 0
initial apicid  : 0
fpu     : yes
fpu_exception   : yes
cpuid level : 13
wp      : yes
flags       : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca
bugs        : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass
bogomips    : 8100.30
TLB size    : 2560 4K pages
clflush size    : 64
cache_alignment : 64
address sizes   : 43 bits physical, 48 bits virtual
power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 1 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 3964.890 cache size : 512 KB physical id : 0 siblings : 12 core id : 1 cpu cores : 6 apicid : 2 initial apicid : 2 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 2 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 3944.263 cache size : 512 KB physical id : 0 siblings : 12 core id : 2 cpu cores : 6 apicid : 4 initial apicid : 4 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 3 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 3743.043 cache size : 512 KB physical id : 0 siblings : 12 core id : 4 cpu cores : 6 apicid : 8 initial apicid : 8 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 4 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 3281.557 cache size : 512 KB physical id : 0 siblings : 12 core id : 5 cpu cores : 6 apicid : 10 initial apicid : 10 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 5 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 3499.477 cache size : 512 KB physical id : 0 siblings : 12 core id : 6 cpu cores : 6 apicid : 12 initial apicid : 12 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 6 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 3873.267 cache size : 512 KB physical id : 0 siblings : 12 core id : 0 cpu cores : 6 apicid : 1 initial apicid : 1 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 7 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 4042.103 cache size : 512 KB physical id : 0 siblings : 12 core id : 1 cpu cores : 6 apicid : 3 initial apicid : 3 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 8 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 3995.767 cache size : 512 KB physical id : 0 siblings : 12 core id : 2 cpu cores : 6 apicid : 5 initial apicid : 5 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 9 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 4044.486 cache size : 512 KB physical id : 0 siblings : 12 core id : 4 cpu cores : 6 apicid : 9 initial apicid : 9 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 10 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 4015.678 cache size : 512 KB physical id : 0 siblings : 12 core id : 5 cpu cores : 6 apicid : 11 initial apicid : 11 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

processor : 11 vendor_id : AuthenticAMD cpu family : 23 model : 8 model name : AMD Ryzen 5 2600X Six-Core Processor stepping : 2 microcode : 0x800820d cpu MHz : 3984.904 cache size : 512 KB physical id : 0 siblings : 12 core id : 6 cpu cores : 6 apicid : 13 initial apicid : 13 fpu : yes fpu_exception : yes cpuid level : 13 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb hw_pstate sme ssbd sev ibpb vmmcall fsgsbase bmi1 avx2 smep bmi2 rdseed adx smap clflushopt sha_ni xsaveopt xsavec xgetbv1 xsaves clzero irperf xsaveerptr arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif overflow_recov succor smca bugs : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass bogomips : 8100.30 TLB size : 2560 4K pages clflush size : 64 cache_alignment : 64 address sizes : 43 bits physical, 48 bits virtual power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

hseara commented on 2019-12-13 11:47 (UTC)

@brisvag Please recompile gromacs. hwloc has been updated from v1 to v2 which brakes gromacs installation. Recompiling gromacs solves the issue.

brisvag commented on 2019-12-10 14:09 (UTC) (edited on 2019-12-10 14:10 (UTC) by brisvag)

When I try to use gmx dump on a .tpr, I get the following error:

gmx: error while loading shared libraries: libhwloc.so.5: cannot open shared object file: No such file or directory

Indeed, the library is missing. Simply adding a symlink to libhwloc.so adding .5 at the end solves the issue. Shouldn't this be handled by the installation?

E3LDDfrK commented on 2019-10-24 17:05 (UTC) (edited on 2019-10-25 23:27 (UTC) by E3LDDfrK)

EDIT 3: A solution here: https://bbs.archlinux.org/viewtopic.php?pid=1870411#p1870411

I have the same error as @mefistofeles.

EDIT 2: And @malinke too. It's partly because my CPU doesn't support AVX2, I think. There's a double "-march=core-avx2 -march=native" when compiling fftw. It fails because my "-march=native" doesn't actually support AVX2.

#error "compiling simd-avx2.h without avx2 support"

I've also changed my /etc/makepkg.conf as @hseara suggested.

It's a Thinkpad X220 with Sandy Bridge, so I used -DGMX_SIMD=AVX_256 on my PKGBUILD. At least in my case, computer doesn't support avx2, so it failed to compile fftw. Not sure what to do here, it seems fftw is automatically compiled with "--enable-avx2". I'll try again later without DGMX_BUILD_OWN_FFTW=ON on the PKGBUILD.

EDIT 1: So it builds successfully when I replaced DGMX_BUILD_OWN_FFTW=ON with -DGMX_FFT_LIBRARY=fftw3 on the PKGBUILD. Not sure if using pacman-installed fftw with GROMACS will lead to problems later on.

For what it's worth, like @mefistofeles, I also tried to manually build the package using cmake and DGMX_BUILD_OWN_FFTW=ON, and it worked. I wonder what the problem is. From what I can tell, gromacs-2019.4/src/external/build-fftw/CMakeLists.txt says it will build fftw with only either just "--enable-sse2" or the whole "--enable-sse2;--enable-avx;--enable-avx2". The "--enable-avx" always comes with "--enable-avx2". But it worked this time, despite my CPU not supporting AVX 2. When running cmake, it also outputted:

The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;--enable-avx;--enable-avx2;--enable-avx512

Just for comparison. This line from manual install succeeds:

libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I/home/user/download/gromacs-2019.4/build/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2 -I../../.. -I /home/user/download/gromacs-2019.4/build/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild -march=core-avx2 -mfma -O3 -fomit-frame-pointer -mtune=native -malign-double -fstrict-aliasing -fno-schedule-insns -MT n1fv_2.lo -MD -MP -MF .deps/n1fv_2.Tpo -c /home/user/download/gromacs-2019.4/build/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_2.c  -fPIC -DPIC -o n1fv_2.o

This line from aur using pikaur fails:

libtool: compile:  gcc-8 -DHAVE_CONFIG_H -I. -I/home/user/.cache/pikaur/build/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2 -I../../.. -I /home/user/.cache/pikaur/build/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild -D_FORTIFY_SOURCE=2 -march=core-avx2 -mfma -march=native -O2 -pipe -fno-plt -MT n1fv_2.lo -MD -MP -MF .deps/n1fv_2.Tpo -c /home/user/.cache/pikaur/build/gromacs/src/double/src/external/build-fftw/fftwBuild-prefix/src/fftwBuild/dft/simd/avx2/n1fv_2.c  -fPIC -DPIC -o n1fv_2.o

So possibly the double "-march" thing makes it fail? Just "-march=core-avx2" vs "-march=core-avx2 -march=native". Because my Sandy Bridge ("-march=native" part) doesn't actually support AVX2.