[gmx-users] Error: illegal instruction (core dumped)
Mark Abraham
mark.j.abraham at gmail.com
Tue Mar 25 11:05:01 CET 2014
On Mar 25, 2014 7:00 AM, "Ly Minh Nhat" <ganuongphap at gmail.com> wrote:
>
> - "does it work? Does it give an error?"
> It's not. The error is:
>
> CMake Error at fftwBuild-stamp/extract-fftwBuild.cmake:11 (message):
> error: file to extract does not exist:
That's impossible if your original cmake command was
cmake ..
from an empty build directory.
Mark
>
> - The output of cat /proc/cpuinfo:
> ooker at ooker-Aspire-4741:~$ cat /proc/cpuinfo
>
> processor : 0
> vendor_id : GenuineIntel
> cpu family : 6
> model : 37
> model name : Intel(R) Pentium(R) CPU P6200 @ 2.13GHz
> stepping : 5
> microcode : 0xd1070214
> cpu MHz : 933.000
> cache size : 3072 KB
> physical id : 0
> siblings : 2
> core id : 0
> cpu cores : 2
> apicid : 0
> initial apicid : 0
> fdiv_bug : no
> f00f_bug : no
> coma_bug : no
> fpu : yes
> fpu_exception : yes
> cpuid level : 11
> wp : yes
> 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 nx rdtscp
lm
> constant_tsc arch_perfmon pebs bts xtopology nonstop_tsc aperfmperf pni
> dtes64 monitor ds_cpl est tm2 ssse3 cx16 xtpr pdcm pcid popcnt lahf_lm
arat
> dtherm
> bogomips : 4255.92
> clflush size : 64
> cache_alignment : 64
> address sizes : 36 bits physical, 48 bits virtual
> power management:
>
> processor : 1
> vendor_id : GenuineIntel
> cpu family : 6
> model : 37
> model name : Intel(R) Pentium(R) CPU P6200 @ 2.13GHz
> stepping : 5
> microcode : 0xd1070214
> cpu MHz : 1199.000
> cache size : 3072 KB
> physical id : 0
> siblings : 2
> core id : 2
> cpu cores : 2
> apicid : 4
> initial apicid : 4
> fdiv_bug : no
> f00f_bug : no
> coma_bug : no
> fpu : yes
> fpu_exception : yes
> cpuid level : 11
> wp : yes
> 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 nx rdtscp
lm
> constant_tsc arch_perfmon pebs bts xtopology nonstop_tsc aperfmperf pni
> dtes64 monitor ds_cpl est tm2 ssse3 cx16 xtpr pdcm pcid popcnt lahf_lm
arat
> dtherm
> bogomips : 4255.92
> clflush size : 64
> cache_alignment : 64
> address sizes : 36 bits physical, 48 bits virtual
> power management:
>
>
> - Using dpkg --list | grep compiler give me the list of installed
> compilers and version:
>
> ii g++
> 4:4.8.1-2ubuntu3 i386 GNU C++
> compiler
> ii g++-4.8
> 4.8.1-10ubuntu9 i386 GNU C++
> compiler
> ii gcc
> 4:4.8.1-2ubuntu3 i386 GNU C
> compiler
> ii gcc-4.8
> 4.8.1-10ubuntu9 i386 GNU C
> compiler
> ii hardening-includes
> 2.3ubuntu1 all Makefile
for
> enabling compiler flags for security hardening
> ii libxkbcommon0:i386
> 0.3.1-1 i386 library
> interface to the XKB compiler - shared library
>
>
>
> On Mon, Mar 24, 2014 at 6:04 PM, Mark Abraham <mark.j.abraham at gmail.com
>wrote:
>
> > I can't delete a post. This is a mailing list, not a forum (even if you
are
> > reading on some half-broken nabble setup, or something).
> >
> > A plain
> >
> > cmake ..
> >
> > from an empty build tree is designed to just work if you then run mdrun
on
> > the same machine. If it doesn't, that's an error we want to fix, but as
> > Justin says we'll need a lot more information about your compiler and
> > hardware.
> >
> > Mark
> >
> >
> >
> > On Mon, Mar 24, 2014 at 10:32 AM, ooker <ganuongphap at gmail.com> wrote:
> >
> > > @Mark Abraham: I have received your email but because I don't see it
on
> > the
> > > thread so I think you deleted your answer. Sorry about that. I'm still
> > new
> > > with the mail list. Anyway, I have already deleted the build folder
and
> > > make a fresh install but it doesn't solve.
> > >
> > > @Justin Lemkul: my machine is Intel Pentium P6200 (2.13 GHz, 3 MB L3
> > > cache). Any cmake command leads to the same error. So if you want a
> > > specific command, let's use the simplist one:* cmake ..*
> > >
> > > I know that I optimized it wrong, but how can I fix that?
> > >
> > >
> > > On Mon, Mar 24, 2014 at 6:11 AM, Justin Lemkul [via GROMACS] <
> > > ml-node+s5086n5015337h88 at n6.nabble.com> wrote:
> > >
> > > >
> > > >
> > > > On 3/23/14, 11:57 AM, ooker wrote:
> > > > > sorry for spamming, but I need to up this thread. I'll delete this
> > > after
> > > > > someone answer. Sorry.
> > > > >
> > > >
> > > > You'll need to provide exact details of your hardware and your exact
> > > cmake
> > > > command, otherwise there's nothing productive to suggest. The build
> > > > machinery
> > > > is good at picking the correct optimization type, so the only real
> > issue
> > > > is if
> > > > you're selecting an optimization that is not supported.
> > > >
> > > > -Justin
> > > >
> > > > --
> > > > ==================================================
> > > >
> > > > Justin A. Lemkul, Ph.D.
> > > > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> > > >
> > > > Department of Pharmaceutical Sciences
> > > > School of Pharmacy
> > > > Health Sciences Facility II, Room 601
> > > > University of Maryland, Baltimore
> > > > 20 Penn St.
> > > > Baltimore, MD 21201
> > > >
> > > > [hidden email] <http://user/SendEmail.jtp?type=node&node=5015337&i=0
>
> > |
> > > > (410) 706-7441
> > > > http://mackerell.umaryland.edu/~jalemkul
> > > >
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