Package Details: gromacs 2022.2-1

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: 21
Popularity: 0.001051
First Submitted: 2011-12-14 17:03 (UTC)
Last Updated: 2022-06-24 15:37 (UTC)

Latest Comments

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.

hseara commented on 2019-06-13 14:46 (UTC)

@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 (UTC) (edited on 2019-05-21 21:27 (UTC) by mefistofeles)

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 (UTC) (edited on 2019-11-08 08:50 (UTC) by hseara)

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 (UTC)

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 (UTC) (edited on 2017-12-04 16:41 (UTC) by hseara)

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.

mefistofeles commented on 2017-12-03 22:53 (UTC)

@malinke I was also getting avx2 errors. Specifically this: error: #error "compiling simd-avx2.h without avx2 support", which some guys at #archlinux think it's an error from upstream. The complete error output is at: https://bpaste.net/show/3bbef4217034 (it may have a short lifetime, sorry)

There one can see that the problem is building the fftw, so I tried removing the -DGMX_BUILD_OWN_FFTW=ON \ lines in the PKGBUILD (lines 51 and 62) and got better results but still errors on testing it. The output I'm getting doing what I said is here: https://bpaste.net/show/01d9d68140bd

BTW, when compiling directly the source code by using cmake and make it builds, with not special options, just as it's shown in: http://web.archive.org/web/20170714101612/http://www.gromacs.org/Developer_Zone/Building_and_Testing/Cmake in the "Configuring with default settings" section. Hope this helps to give ideas on how to make gromacs build using this PKGBUILD/AUR?

hseara commented on 2017-10-01 11:00 (UTC)

@malink "(I didn't care if I had a avx build or not)" You should care. mdrun will be 2x to 4x faster if compiled with avx (depending on the version) activated. My fix will activate the highest level of avx by default. My fix will allow also CUDA support if available. This is why we need gcc5. CUDA 9 does not seem to solve this issue. In any case, thanks for your comment as the fix simplifies the installation.

malinke commented on 2017-10-01 07:33 (UTC)

I read the avx instructions. My build problem was that the default pkgbuild would fail since gromacs cmake config tried to enable avx and the global flags in `/etc/makepkg.conf` deactivated it later resulting in a build error (I didn't care if I had a avx build or not). The changed cflags in the current version fix that.

hseara commented on 2017-09-24 15:39 (UTC)

@mailkinke please read the content of the PKGBUILD file. There it is clearly stated: ###### CMAKE OPTIONS DISABLE BY DEFAULT ########### # If you are using an AVX2 capable CPU, you will # # not have AVX2 binaries unless you set -march to # # 'native', your respective architecture flag: # # https://gcc.gnu.org/onlinedocs/gcc-5.3.0/gcc/x86-Options.html#x86-Options # # or just include '-mavx2' to the default compiler# # flags in the /etc/makepkg.conf: # # https://wiki.archlinux.org/index.php/Makepkg#Architecture.2C_compile_flagsAdd # ###################################################

hseara commented on 2017-09-24 15:38 (UTC)

@malinke: Currently compiling CUDA against gcc7 is not possible. If you are not using Cuda, feel free to comment the lines where we change the compiler and their options in the PKGBUILD file.

malinke commented on 2017-09-21 13:37 (UTC)

One problem is that in `/etc/makepkg.conf` the cflags and cxxflags contain `-march=x86_64 -mtune=generic`. These flags are not used by gromacs to determine if avx should be activated during the configuration stage of cmake. Therefore gromacs tries to build with avx instructions (on my machine). This results in the following flags to the c/c++ compiler '-march=cpu-avx -march=x86_64 -mtune=generic'. This breaks the builds as only the last usage of `march/tune` is using deactivating the avx build. The build then stops complaining it doesn't know about the avx functions. Overwritting the flags in the PKGBUILD lets the compilation finish. These cflag I have are the standard for every user. https://git.archlinux.org/svntogit/packages.git/tree/trunk/makepkg.conf?h=packages/pacman

malinke commented on 2017-09-21 12:31 (UTC)

Gromacs doesn't build with gcc5. Using gcc5 I get the following error. ``` gcc-5: error: unrecognized command line option ‘-fno-plt’ ``` I had no problem building and running gromacs with gcc7

hseara commented on 2017-09-13 17:23 (UTC) (edited on 2017-09-24 15:35 (UTC) by hseara)

Compiling gromacs with CUDA support will fail after the update to glibc-2.26. This is incompatible with CUDA 8 and it is not clear whether the soon to come CUDA 9 will solve this problem. (NEWS: A dirty fix implemented in the CUDA package allows again the compilation).

hseara commented on 2017-04-28 16:42 (UTC) (edited on 2017-09-24 15:34 (UTC) by hseara)

At least for Nvidia, Gromacs detects CUDA capable cards. If you have CUDA installed, it then includes CUDA capability without the need of using any flag. This default behavior makes the current Gromacs installation platform agnostic. I do not wish to enable any flag that can potentially change this platform independent behavior. If Gromacs does not by default activate in your system OpenCL, please write a bug report to Gromacs people, so they provide similar functionality as for CUDA. You can always edit the PKGBUILD before installing to include your flags. Besides, you will need to tell gromacs to use your compilers.

jaw8621 commented on 2017-04-27 11:44 (UTC)

Now that LLVM and Clang 4.0 is out, gromacs should have the cmake OpenCL compile flags turned on by default. Works since gromacs 5.1 and with both, amd and nvidia as soon as a suitable gpu and driver is present. Flags: -DGMX_GPU=ON -DGMX_USE_OPENCL=ON

jaw8621 commented on 2017-02-27 19:53 (UTC)

ah thanks. Sorry for my ignorance. New to the arch world :) I think to clarify this, the message should read something like this: ###### CMAKE OPTIONS DISABLE BY DEFAULT ########### # If you are using an AVX2 capable CPU, you will # # not have AVX2 binaries unless you set -march to # # 'native', your respective architecture flag: # # https://gcc.gnu.org/onlinedocs/gcc-5.3.0/gcc/x86-Options.html#x86-Options # # or just include '-mavx2' to the default compiler# # flags in the /etc/makepkg.conf: # # https://wiki.archlinux.org/index.php/Makepkg#Architecture.2C_compile_flagsAdd # ################################################### (Sorry, turned out to be a little longer ;)) to avoid confusion. Right now it makes you think it is set to native when instead it says something x86. Obviously one can just look up /etc/makepkg.conf and find the obvious...

hseara commented on 2017-02-27 12:56 (UTC)

The issue is not when you have -march=native. The issue is when you use the default /etc/makepkg.conf file which contains "-march=x86-64 -mtune=generic" in AVX2 capable computers. Multi-core compilation is configured in your /etc/makepkg.conf as in any other package. For example, I have MAKEFLAGS="-j12".

jaw8621 commented on 2017-02-26 16:51 (UTC) (edited on 2017-02-26 16:52 (UTC) by jaw8621)

what is the issue with: ###### CMAKE OPTIONS DISABLE BY DEFAULT ########### # If you are using a haswell CPU, you will have # # problems compiling with AVX2 support unless you # # modify march=native in the /etc/makepkg.conf: # # https://wiki.archlinux.org/index.php/Makepkg#Architecture.2C_compile_flagsAdd # ################################################### ? I compile on a haswell machine with -march=native and it produces a correct AVX2 executable. Are newer than haswell architectures also supposedly affected? And how about compiling on more then 1 core to speed up compile times?

hseara commented on 2016-07-14 20:00 (UTC)

NOTE: PROBLEMS BUILDING GROMACS AFTER GCC6 UPDATE WITH CUDA SUPPORT If your system has CUDA installed, gromacs installer by default will try to compile with CUDA support. Unfortunately, currently gcc6 and CUDA do not play well along and the compilation will fail. Because of this the later cuda release comes along with gcc5 package. Using gcc5 we can again build gromacs in bash using the following commands: export CC=gcc-5 export CXX=g++-5 makepkg

hseara commented on 2016-07-14 19:53 (UTC)

Sorry, I'm not sure I'm understand really your problem. This package is the default gromacs and as such is installed in: /usr/bin /usr/include /usr/lib /usr/share I just build the package and it works perfectly with the files installed in above directories. Are you sure that you are installing gromacs and not aur/gromacs-5.0-complete or aur/gromacs-4.6-complete which indeed install this version of gromacs in /usr/local. In this latter packages the intention is that they can coexist with the last stable version in case your projects still require them and because of that they are encapsulated in /usr/local/gromacs-XXX/ If your problems persist please provide more details.

sebstar commented on 2016-07-14 08:55 (UTC)

Thanks for the PKGBUILD! There's one odd thing though. Am I the only one whose installation prefix specification is totally ignored by Cmake? In build() cmake is run with -DCMAKE_INSTALL_PREFIX=/usr/. But that is totally ignored, as is revealed during package(): gromacs was still installed into ${pkgdir}/usr/local/gromacs, not ${pkgdir}/usr, so I had to replace all instances of /usr with /usr/local/gromacs.

hseara commented on 2015-07-15 12:21 (UTC)

1) Now tests are run by default. If you do not want them comment out the "make check" lines. 2) License has been corrected to LGPL 3) Specific SIMD is not longer enforced. Gromacs will detect the best for your system. If you have any problem with this modify march=native in the /etc/makepkg.conf 4) I have cleaned the PKGBUILD and some options which are default 5) I will like to keep both double and single compilation together as many times double are also required especially for minimizing. In the future we might consider a separated split package. 6) I want to minimize the usage of AUR-libraries, that's why I won't make default fftw-bettersimd. You can also make another package, Eg. gromacs-fftw-bettersimd, to incorporate your changes if you want to.

commented on 2015-07-14 20:15 (UTC)

FYI any who are trying to enable tests replace "make test" with "make check".

commented on 2015-07-14 20:07 (UTC)

Thanks for the response. Concerning the test, don't comment out "make test", because that is not the correct command. Just replace it with "make check".

commented on 2015-06-25 01:27 (UTC)

Here's my suggested PKGBUILD: https://gist.github.com/wesbarnett/6d521b66301ebe9eb786 Then people can follow the wiki article if the want double precsion, MPI, GPU, etc.

commented on 2015-06-16 23:46 (UTC)

Sorry to keep commenting, the license should be LGPL, not GPL. Also "make check" works for me, not "make test".

commented on 2015-06-16 23:10 (UTC)

A GROMACS-enhanced fftw library is now available in AUR as "fftw-bettersimd". Also a few thoughts: GROMACS should detect the appropriate SIMD instructions for your processor, so that flag probably doesn't need to be set. Also, is -DGMX_OPENMP a real flag? I can't find it in the documentation. I also think that a better default would be better to just have it compile for single precision, since most people don't need double precision. I'm currently working on the GROMACS wiki page.

commented on 2015-06-16 23:10 (UTC)

A GROMACS-enhanced fftw library is now available in AUR as "fftw-bettersimd". Also a few thoughts: GROMACS should detect the appropriate SIMD instructions for your processor, so that flag probably doesn't need to be set. Also, is -DGMX_OPENMP a real flag? I can't find it in the documentation. I also think that a better default would be better to just have it compile for single precision, since most people don't need double precision. I'm currently working on the GROMACS wiki page [[GROMACS|here]].

commented on 2015-06-16 22:54 (UTC)

One other thing - you shouldn't have to set SIMD instructions unless you get an error, so that probably should be removed. By default GROMACS chooses the best (http://www.gromacs.org/Documentation/Installation_Instructions_5.0#simd-support).

commented on 2015-06-16 20:08 (UTC)

One suggestion - the current PKGBUILD has both single and double precision enabled by default. I think a more "sane" default would just be single precision since according to the GROMACS site double precision is "slower, and not normally useful." (http://www.gromacs.org/Documentation/Installation_Instructions_5.0#typical-gromacs-installation)

commented on 2015-06-15 13:44 (UTC)

A GROMACS-enhanced fftw library is now available in AUR as "fftw-bettersimd".

hseara commented on 2015-06-02 20:24 (UTC)

Thanks for the tip. I was always wondering how come none of the gromacs developers where unaware of this problem. Now, I see. The problem was in my side. I will add this tip in the next release.

necomancer commented on 2015-05-30 03:56 (UTC)

@hseara If you are using a haswell CPU, modify march=native in the /etc/makepkg.conf: https://wiki.archlinux.org/index.php/Makepkg#Architecture.2C_compile_flags would sovle the problem, anyway, the gromacs recommends AVX2_256 enabled if a haswell CPU was used.

commented on 2015-05-24 02:03 (UTC)

5.0.5 has been released

hseara commented on 2015-01-13 12:15 (UTC)

IMPORTANT NOTE: - if you have a rather new INTEL CPU you might encounter that gromacs does not compile spiting errors related to AVX2_256. They look like this: ##### /tmp/yaourt-tmp-hector/aur-gromacs/src/gromacs-5.0.4/src/gromacs/simd/vector_operations.h:157:1: note: The ABI for passing parameters with 32-byte alignment has changed in GCC 4.6 gmx_simd_iprod_d(gmx_simd_double_t ax, gmx_simd_double_t ay, gmx_simd_double_t az, ^ In file included from /usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/include/immintrin.h:41:0, from /tmp/yaourt-tmp-hector/aur-gromacs/src/gromacs-5.0.4/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40, from /tmp/yaourt-tmp-hector/aur-gromacs/src/gromacs-5.0.4/src/gromacs/simd/simd.h:118, from /tmp/yaourt-tmp-hector/aur-gromacs/src/gromacs-5.0.4/src/gromacs/gmxlib/bondfree.c:62: /tmp/yaourt-tmp-hector/aur-gromacs/src/gromacs-5.0.4/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h: In function ‘gmx_simd_cvt_dib2db_avx2_256’: /usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/include/avxintrin.h:1441:1: error: inlining failed in call to always_inline ‘_mm256_castpd128_pd256’: target specific option mismatch _mm256_castpd128_pd256 (__m128d __A) ... #### If this is your case just edit both cmake commands, one for sigle another for double precision, in the build function with: -DGMX_SIMD=AVX_256

dotsdl commented on 2014-12-28 16:15 (UTC)

Thanks duca for establishing and maintaining this pkgbuild! It's been a real help. Thanks to hseara for taking it up!

duca commented on 2014-12-26 16:27 (UTC)

Guys, I am transfering this package to hseara. He's been doing most of the work keeping a functional pkgbuild already. I was the first post of a pkgbuild for gromacs back in the 4.0.x days and i'm confident that it'll be on good hands.

hseara commented on 2014-12-09 10:45 (UTC)

Please, update the package with the fix below. Right now does not build.

poluyan commented on 2014-11-28 15:53 (UTC)

Thank you, eomarjee. Now it builds successfully! Hope that the original PKGBUILD file will be modified.

commented on 2014-11-28 10:00 (UTC)

47c47 < install -D -m755 ${srcdir}/${pkgname}-${pkgver}/scripts/completion.bash "${pkgdir}/usr/share/bash-completion/completions/gromacs" --- > install -D -m755 ${srcdir}/${pkgname}-${pkgver}/src/programs/completion/gmx-completion.bash "${pkgdir}/usr/share/bash-completion/completions/gromacs"

Methylzero commented on 2014-11-07 10:59 (UTC)

This package has failed to build on my system. I am not sure why. -- Installing: Creating symbolic link /tmp/yaourt-tmp-manjarouser/aur-gromacs/pkg/gromacs/usr/bin/g_wheel_d install: cannot stat ‘/tmp/yaourt-tmp-manjarouser/aur-gromacs/src/gromacs-5.0.2/scripts/completion.bash’: No such file or directory ==> ERROR: A failure occurred in package().

duca commented on 2014-07-04 13:59 (UTC)

In the lab i work we dont usually even update unless an important bug is found on the one we use or some important feature is released with a new version. Our upgrade from 3 to 4 was quite bumpy and even within the first releases of the 4 series. Anyway thank you for your feedbacks, guys.

hseara commented on 2014-07-02 05:27 (UTC)

Please do not update to gromacs5 until the developers consider it suitable for production runs. Right now this is not the case. Notice for example the note in the download section where clearly states: "Please note that these are not yet regarded as production quality, pending further testing, but the code is now feature-stable." In my humble opinion and with the experience in the transition from gromacs3 to gromacs4 it will take at least one or more releases to be safe to use for production quality runs. I think we should wait until then a bit for the update and in the mean while keep in the 4.6 branch. Soon there will be an update 4.6.6 will includes all bug fixes in gromacs5.

dotsdl commented on 2014-07-02 00:55 (UTC)

Gromacs 5.0 just came out a couple of days ago; no rush, but I flagged the package as out of date for this reason.

duca commented on 2013-04-26 03:06 (UTC)

Sorry for the delay

hseara commented on 2013-04-18 15:19 (UTC)

Hi, it is the second time I put out of date the package. Please update it.

commented on 2013-04-08 08:34 (UTC)

Hi, after running into some problems like missing permission to edit /pkg and folders getting created to early, i had to modify the PKGBUILD. If anyone has similar problems, maybe this can help: http://codepad.org/gmVjykgp This is my first PKGBUILD, so please tell me if something could be done better.

quizzmaster commented on 2012-11-24 23:30 (UTC)

May you add the fix for usind do_dssp with last dssp version? Thats the way i did it: git clone git://git.gromacs.org/gromacs.git git checkout --track -b release-4-5-patches origin/release-4-5-patches

duca commented on 2012-05-14 19:52 (UTC)

@josephgbr Thanks for sharing the new completion directory. hseara added ckame to makedepends completion.* is there due to gromacs dev discretion but the new package will remove them (it was like this a awhile ago). @hseara a) I got your point, i misread your previous pkgbuild. b) I had this problem a while ago and never and never tried again using n>4. c) This is not my assumption, it's an upstream assumption (just check your /etc/profile.d and you'll see only .csh and .sh files in there). I dont mind moving all GMXRC.* scripts to that location (and patch GMXRC to updated location of GMXRC.*) and let /usr/bin with only gromacs executables At first i thought you were just having your time because of my comments on your package, but i do not think like this anymore. Actually i appreciate your comments, they help me improve the quality of my packages in the end.

hseara commented on 2012-05-12 08:45 (UTC)

Here is the new PKGBUILD with cmake in makedepends http://codepad.org/VLnCPrEJ PD: Our packages have been already merged

rafaelff commented on 2012-05-12 08:01 (UTC)

Some comments on this package: * 'cmake' is missing in makedepends. * if you decide to use doxygen, then add it to makedepends as well * 'bash-completion' directory changed to /usr/share/bash-completion/completions/ (WTH is /usr/bin/completion.* doing in /usr/bin ?)

hseara commented on 2012-05-12 00:42 (UTC)

I will try to answer in order: a) No you are wrong you don't need two copies. Cmake copies everything you need to the single and double directory. Please realize that you make make installs in them. Please read carefully the PKGBUILD I sent you because I have the feeling you did not understand the point. Moreover, I have tested it and it works perfectly. If not please let me know what is the problem. b) Regarding -j2, David van der Spoel, Ph.D. one of the main gromacs developer compiles gromacs with 32 cores, at least it is what he always says. Myself I have always, more than 10 years, compile with the maximum amount of cores and I have never seen a problem. If you see any problem please fill a bug report upstream as it is really an important issue that no one I know so far has encounter. So unless you can backup your claim you should definitely remove "-j2". c) Regarding GMXRC. You are assuming that everybody uses bash as a main interpreter. It is very likely that you are right but it might not be the case. The beauty of sourcing in /etc/profile.d/GMXRC is that it will select the appropriated script for the used interpreter. By the way be aware that this files are changed in the compilation to match the installation paths. That's why I use the move command. So I do not understand the problem you expose, but if you know any other better way to do the same I do not have any problem. d) Yes, we definitely need to merge this two packages. I will ask the merge tomorrow. Thanks, and please do not see in my comments any bad intentions. I just want to help to have the best package for everybody.

duca commented on 2012-05-11 14:56 (UTC)

Strange, the suffixes in this release are definatelly a typo for the first thing i did was to remove them all. I believe while i was adding the comments i brought them back. Aesthetically i agree that the cleaner the better, not many packages out there are clean in the sense of number of lines nor in their solutions to correctly build their packages. If you follow the discussion list you have alredy read some debate. But in this case if you run cmake (and make) twice before 'make install', it will remove the previous 'make' and you lose half of the work so separating single and double sources is required. Does it compile correctly using 12 cores? Using 8 or 16 on some of our machines the resulted binnaries were buggy and for that reason i added -j2 a long time ago before gromacs was first added to COMMUNITY (and never taken them away hehe) and kept -j'n' in makepkg.conf to build other packages that were not problematic. I agree with the merge, but MV is not the adequate solution to send GMXRC to profile.d and GMXRC is supposed to be a script which sources GMXRC.bash or else. I could patch GMXRC to install the correct script (to profile.d) instead of sourcing it and run it using a 'post install' directive (gromacs.install) or add GMXRC.csh and GMXRC.bash to profile.d as some packages do (firefox and xorg-server for instance).

hseara commented on 2012-05-10 14:44 (UTC)

Regarding the doxygen documentation, I will definitely make a different package. The issue is that I'm not sure if there is any official rules for placing such documentation. So I guess any guess that you make is as good as mine.

hseara commented on 2012-05-10 14:40 (UTC)

I have revised your changes and simplified some redundant lines and clean all commented code of from the PKGBUILD. You can find the PKGBUILD in the following link: http://codepad.org/3AYnhgHC Just a note. In AUR the packages should be as clean as possible and you must agree that this is much more clean that yours (Easy to read). Besides, the part you commented out is never going to be used by anybody, at least in my opinion, and difficult significantly the reading. Most likely, nobody will even understand what is the propose of this lines besides you and me. If you really want to make it useful I think you should better consider to make different packages for each of the gromacs versions available as I have done. Still I continue saying that putting suffixes is a pretty bad idea as you limit the usage of scripts and changing between gromacs versions is as easy as sourcing the correspondent GMXRC file. I have also taken away the -j2 from the make line as this has to be configured in /etc/makepkg.conf and changes with each one computer. For example, with your setup I only use two cores out of the 12 that my computers have :). You don't have to copy the data to a different directory. cmake does everything for you. I moved GMXRC to /etc/profile.d/ after compilation. This is very important as will certainly set properly all the libraries, otherwise in certain occasion I get some compiling errors when programming against gromacs. Moreover, it allows you to reset the gromacs in case you use different versions: "source /etc/profile.d/GMXRC" If you agree with all this changes I will merge the gromacs-complete package with yours as they will be now completely equivalent and there is not sense to maintain both. Thanks in advance.

duca commented on 2012-05-09 14:55 (UTC)

Hello hseara, i appreciate the comments and i understand your concerns. To address each one I was trying to find a way to let users update their packages without having to uninstall the previous one, since i did not find anything (nor had the time to search decently for a solution) i agree the scheme is convoluted and, therefore, unnecessary but i'll leave some of the original lines commented as reference in case someone (as i will probably do) decides to install different versions in /usr/local. Being the main package (i am not very fond of the term) it is required to be under /usr (not /usr/local) so you are right about this one. And what about the doxygen documentation?

hseara commented on 2012-05-09 08:55 (UTC)

After the recent changes in your package is not really usable for many of us. I hope I can make myself clear. First you have added suffixes to the binaries. This detail that you might find important to identify the used version lead to two problems. A) The most important, scrips calling the executable by their normal names do not work, e.i. mdrun->mdrun_455. So I'm afraid I will have to continue using my own versions of gromacs for real job, I don't want to have to edit the scripts every time there is a new gromacs version. B) The people that installs the package and do not know what you have in mind gets confuse by the strange naming scheme, e.i. They can not follow any gromacs tutorial. And aside is not really needed because gromacs when you execute any of its executables tells which version is being used. The second problem is the installation path. You are now putting everything in "/usr/local" as I'm doing. As you know that goes against the arch ways. I would like to propose you the following: let's keep your package as the main one containing the latest version installed in "/usr" and without sufixes (Only "_d"), and aside we can make new packages with different gromacs versions that can be installed in "/usr/local" and therefore do not interfere with the main package, your package. In this way I guess everybody will be happy as to use them you only have to source /usr/local/gromacs/gromacs-x.x.x/bin/GMXRC.{bash,sh,zsh}. What do you think?

duca commented on 2012-04-11 17:32 (UTC)

Now gromacs is installed on a private directory under /usr/local/gromacs_version with custom binary and scripts names (bash completion and profile). It does not make use of mpi in this version, only threads.

duca commented on 2012-02-16 20:30 (UTC)

Actually I included the hseara changes and added a few improvements of my own a while back. Unless i forgot something and it this is the case, point me to what i missed :)

xyproto commented on 2012-02-15 16:43 (UTC)

Great initiative hseara. Just leave a comment to me on either package if you come to an agreement with duca, and I can merge them. For the record, I'm for /usr and against /usr/local, if that is possible, since that's the standard for Arch packages, if that does not inconvenience the user too much.

hseara commented on 2012-02-15 10:58 (UTC)

Hi, I did not realized until now that gromacs was kick out from [community].Why don't we merge both packages, mine[gromacs-complete] and yours [gromacs]. In this case, I don't see any inconvenient to change the intallation directory to /usr instead of /usr/local that right now point out my configuration file. Have a look in my PKGBUILD if you agree and we can arrange the details of the merge. I personally prefer to have both single and double precision. Also might be interesting to add the doxygen documentation or this as well as the sources can be a different package.

duca commented on 2012-01-05 21:47 (UTC)

Perhaps you should document better (by a .install script maybe?) how you switch between versions because there's an expected set of locations and what you used. Please take no offense in my previous message cause i dont mean any. How most of 'normal' users use gromacs (and i work with it for a long time by now) is not subject to assumption. Populating /usr/local is not against the fhs as AL implements it. NOTE ASIDE: I dont recal my different installed versions interfering with each other (i have 3.3.3 and 4.0.7 on most of the lab machines).

hseara commented on 2011-12-27 09:24 (UTC)

There are two reasons. The first is to make it compatible with the community gromacs package. This package installs both single and double precision executable. Therefore the single precision executables will conflict with the official gromacs package. Right now I do not want to add this package as a replace or conflict of the community package. Still just to be consistent between installed versions of single and double precision I want to install both. The second reason is that I use intensively gromacs for my work and because of its porpoise I often require to have installed different versions (most of normal users have this need). I want to remind at this point that this is a publication quality scientific software and changing the versions inside a given project can introduce some uncertainties when comparing between systems (That's a pity but it is the reality). Having it as a whole in /usr/local/gromacs/gromacs-x.x/ allows you to use a given version easy by sourcing the /usr/local/gromacs/gromacs-x.x/bin/GMXRC.bash file, this file in the community gromacs version is deleted. This difficult significantly the usage of different gromacs versions and for normal users the workflow in general. NOTE ASIDE: My installer uses CMAKE for building and not MAKE which is deprecated and might disappear at any time in a future version.

duca commented on 2011-12-26 21:05 (UTC)

Hello hseara, Is there any particular reason to prefix it to /usr/local when the archlinux default is /usr.

xyproto commented on 2011-12-14 17:26 (UTC)

Moved from [community] in connection with the Christmas Cleanup https://wiki.archlinux.org/index.php/Christmas_Cleanup.