[gmx-users] Error: illegal instruction (core dumped)
Ly Minh Nhat
ganuongphap at gmail.com
Wed Apr 2 17:19:04 CEST 2014
Thank you Mark Abraham and Justin Lemkul. I know that I haven't responded
for a week and it shouldn't be but I come back to say that I have found the
solution. I want to share this link so maybe it will help someone after me.
Thank you so much for spending your time to help me. I'm honestly
appreciate that.
http://gromacs.5086.x6.nabble.com/How-to-provide-the-FFTW3-install-directory-tt5015481.html
Good luck to you :D
On Tue, Mar 25, 2014 at 5:04 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
> 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
> > > > >
> > > > > ==================================================
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > > > > send a mail to [hidden email]<
> > > > http://user/SendEmail.jtp?type=node&node=5015337&i=1>.
> > > > >
> > > > >
> > > > >
> > > > > ------------------------------
> > > > > If you reply to this email, your message will be added to the
> > > discussion
> > > > > below:
> > > > >
> > > > >
> > > >
> > >
>
> http://gromacs.5086.x6.nabble.com/Error-illegal-instruction-core-dumped-tp5015293p5015337.html
> > > > > To unsubscribe from Error: illegal instruction (core dumped),
> click
> > > > here<
> > > >
> > >
>
> http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=5015293&code=Z2FudW9uZ3BoYXBAZ21haWwuY29tfDUwMTUyOTN8MjA5NTYxNDQyOQ==
> > > > >
> > > > > .
> > > > > NAML<
> > > >
> > >
>
> http://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml
> > > > >
> > > > >
> > > >
> > > >
> > > > --
> > > > View this message in context:
> > > >
> > >
>
> http://gromacs.5086.x6.nabble.com/Error-illegal-instruction-core-dumped-tp5015293p5015343.html
> > > > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-usersor
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list