Package Details: gromacs 2020.4-1

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/
Licenses: LGPL
Submitter: xyproto
Maintainer: hseara
Last Packager: hseara
Votes: 20
Popularity: 0.000873
First Submitted: 2011-12-14 17:03
Last Updated: 2020-10-14 19:35

Dependencies (12)

Required by (1)

Sources (1)

Latest Comments

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E3LDDfrK commented on 2020-03-24 08:27

@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

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

@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

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

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.

hseara commented on 2019-06-13 14:46

@mefistofeles, either your cpu does not support AVX2 (check in /proc/cpuinfo) or your /etc/makepkg.conf is not set to native architecture:

CFLAGS="-march=native -O2 -pipe -fno-plt"
CXXFLAGS="${CFLAGS}"

PS: -fstack-protector-strong in makepkg.conf is not needed

mefistofeles commented on 2019-05-21 20:42

For some reason using the following PKGBUILD fails compiling, check https://paste.rs/IqF

The error is in https://paste.rs/6W0

Specifically the part that says error: #error "compiling simd-avx2.h without avx2 support" when compiling FFTW.

The funny thing is that when I manually compile using "cmake .. -DGMX_GPU=ON -DGMX_SIMD=AVX2_256 -DGMX_BUILD_OWN_FFTW=ON" it works fine. Don't really know what is causing the error. Help appreciated.

BTW, using the -fstack-protector-strong in makepkg.conf didn't work. as suggested by @hseara

hseara commented on 2019-04-15 20:13

No longer needed in gromacs 2019.4

Installation notes

With cmake update to v3.14.x, gromacs is no longer capable of identifying correctly the CPU and therefore the appropriated SIMD level for compilation. If you want to compile gromacs with SIMD while the problem is not solved add the following option to PKGBUILD:

-DGMX_SIMD={AVX_128_FMA, AVX_256, AVX2_256, AVX2_128, AVX_512}

The KEYWORD depends on the SIMD support provided by your CPU.

Usage notes
source /etc/profile.d/GMXRC.bash

roina commented on 2017-12-17 12:35

hseara, the current (2016.4 released September 15, 2017) doesn't works with CUDA in old systems. But new gromacs (2018-beta2 released December 12 2017) works perfectly with current PKGBUILD (gromacs 2016.4-2) and CUDA 9.1. So don't wait and update the version.

hseara commented on 2017-12-04 15:30

The current PKGBUILD works perfectly in new systems.

@manlinke: I have the feeling that at least part of your problem is Cuda related. You seem to have an "NVIDIA GeForce GTX 550 Ti" which is no longer supported by Cuda 9. That means that your code will compile well, but tests will fail. The only possible workaround which I'm using on an old system myself is to use Cuda 8 in your system instead of Cuda 9. It is not possible for me to deal with this issue as it is graphics card dependent. You can always disable CUDA "-DGMX_GPU=OFF".

@manlike: The following lines overriding the /etc/makepkg.conf defaults should take care of the avx2 issues:

export CFLAGS="-march=native -O2 -pipe -fstack-protector-strong"

export CXXFLAGS="${CFLAGS}"

Once you fix the Cuda issues, please check again if you have really avx2 issues.