[Debichem-devel] Bug#725013: [Support] Bug#725013: gromacs-openmpi: grompp crashes with invalid opcode

[Vassilis Virvilis]

On 10/01/2013 09:39 PM, Nicholas Breen wrote:
> Could you please check if the i5 machines where it works include "avx" in the
> flags line of /proc/cpuinfo?
>

yep it has. This is my i5. It is indeed newer than sandy bridge.

bill at beyonder:~$ grep avx /proc/cpuinfo
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe 
syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl 
xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor 
ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic 
popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm arat epb 
xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase 
smep erms
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe 
syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl 
xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor 
ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic 
popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm arat epb 
xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase 
smep erms
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe 
syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl 
xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor 
ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic 
popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm arat epb 
xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase 
smep erms
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge 
mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe 
syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl 
xtopology nonstop_tsc aperfmperf eagerfpu pni pclmulqdq dtes64 monitor 
ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic 
popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm arat epb 
xsaveopt pln pts dtherm tpr_shadow vnmi flexpriority ept vpid fsgsbase 
smep erms


> I built 4.6.3-4 on a different machine than usual, and I think it accidentally
> picked up a CPU optimization it should not have had.  AVX extensions were only
> added on the Sandy Bridge and newer model Intel CPUs, and the Xeon you provided
> the information for doesn't have it.  If that's the case, I will ask for the
> package to be rebuilt on a different machine where that problem won't occur.
>

One question though. When I build with dpkg-buildpackage it was 
crashing. Shouldn't pick the correct flags when I created the packages?

I just retested and I know why. I had the package shared libraries 
installed. So when I tried to run build/src/kernel/grompp it crashed 
because it was using the system's libraries and not the compiled ones.

Ok. So I recompiled and installed my debs and it is working now.

Waiting for your update

-- 

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Vassilis Virvilis Ph.D.
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