[gmx-users] Error: illegal instruction (core dumped)
Ly Minh Nhat
ganuongphap at gmail.com
Tue Mar 25 06:54:36 CET 2014
- "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:
- 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>
> |
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> > > http://mackerell.umaryland.edu/~jalemkul
> > >
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