[gmx-users] segfault on Gromacs 4.6.3 (cuda)

[Mark Abraham]

OK, it's your funeral - but you only need the compiler on the machine
that builds GROMACS, and that compiler doesn't have to be installed in
root file space.

Mark

On Wed, Sep 11, 2013 at 10:32 PM, Guanglei Cui
<amber.mail.archive at gmail.com> wrote:
> I appreciate your comments/suggestions, Mark. But trust me ... everything
> may become "rocket science" when you work for a company with ~10,000
> employees.
>
> Cheers,
>
>
> On Wed, Sep 11, 2013 at 3:23 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> Hi,
>>
>> There's simply no way you can expect compilers more than three years
>> old (icc 11, gcc 4.4) to work seamlessly and produce high performance
>> with brand-new hardware and code. That's like working on a Formula One
>> car with a flint axe. Installing a new compiler is not rocket science!
>>
>> Mark
>>
>>
>> On Tue, Sep 10, 2013 at 2:03 AM, Guanglei Cui
>> <amber.mail.archive at gmail.com> wrote:
>> > Hi Szilard,
>> >
>> > Thanks again for getting back. You may remember the previous thread I
>> > started on regression test failure with icc 11.x compiled binary. Falling
>> > back to SSE2 is my solution, and binaries compiled this way are able to
>> > pass all regression tests, including the one with GPU switched on.
>> However,
>> > it is not clear to me if the GPU part is specifically tested in the
>> > regression.
>> >
>> > As I was trying to explain in the original email, the binary works fine
>> on
>> > a node with proper graphics driver, but crashes on a node where the
>> > graphics driver is older than the CUDA SDK used in compilation. I think
>> > updating the driver may potentially enable the GPU part. Pure CPU
>> > calculation with the same binary seems not working. It is not clear to me
>> > if this is caused by the compiler. It's not really simple to update the
>> gcc
>> > to 4.7 or greater since we use CentOS 5.x in the company. Even CentOS 6.x
>> > uses gcc 4.4.x as default.
>> >
>> > I've just tested the code with -nb cpu. It still crashes. The binary
>> > compiled without GPU works as expected and passed all regression tests.
>> For
>> > now, I can keep separate binaries for GPU and CPU applications before I
>> can
>> > get gcc 4.7 or greater installed.
>> >
>> > Best regards,
>> > Guanglei
>> >
>> >
>> > On Mon, Sep 9, 2013 at 4:35 PM, Szilárd Páll <szilard.pall at cbr.su.se>
>> wrote:
>> >
>> >> HI,
>> >>
>> >> First of all, icc 11 is not well tested and there have been reports
>> >> about it compiling broken code. This could explain the crash, but
>> >> you'd need to do a bit more testing to confirm. Regading the GPU
>> >> detection error, if you use a driver which is incompatible with the
>> >> CUDA runtime (at least as high API version, see the mdrun log header's
>> >> last two lines) and at the moment, some of such cases are not detected
>> >> particularly gracefully.
>> >>
>> >> A few things to try:
>> >> - use gcc, 4.7 is as fast or faster than any icc;
>> >> - run with the "-nb cpu" option; does it still crash?
>> >> - run with GPU detection completely disabled*
>> >> - run the regressiontests; try using CPUs only*
>> >>
>> >> *You can set the GMX_DISABLE_GPU_DETECTION environment variable to
>> >> completely disable the GPU detection.
>> >>
>> >> Cheers,
>> >> --
>> >> Szilárd
>> >>
>> >>
>> >> On Mon, Sep 9, 2013 at 9:52 PM, Guanglei Cui
>> >> <amber.mail.archive at gmail.com> wrote:
>> >> > Dear GMX users,
>> >> >
>> >> > I recently compiled Gromacs 4.6.3 with CUDA (Intel compiler 11.x,
>> SSE2,
>> >> and
>> >> > CUDA SDK 5.0.35). I was doing a test run with simply 'mdrun -deffnm
>> >> > eq2_npt_verlet' (letting mdrun figure out what to use). I received the
>> >> > error telling me my graphics driver was older than the CUDA SDK, and
>> >> > regular CPU code would be used instead. Then, it crashed with
>> >> Segmentation
>> >> > Fault. The code runs properly on another node where the graphics
>> driver
>> >> is
>> >> > more up to date. I wonder if the crashing is somewhat expected, and
>> >> > therefore I should prepare different binaries based on  the
>> capabilities
>> >> of
>> >> > different nodes. Thanks.
>> >> >
>> >> > Best regards,
>> >> > --
>> >> > Guanglei Cui
>> >> > --
>> >> > gmx-users mailing list    gmx-users at gromacs.org
>> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> > * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >> > * Please don't post (un)subscribe requests to the list. Use the
>> >> > www interface or send it to gmx-users-request at gromacs.org.
>> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >> --
>> >> gmx-users mailing list    gmx-users at gromacs.org
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> >> * Please don't post (un)subscribe requests to the list. Use the
>> >> www interface or send it to gmx-users-request at gromacs.org.
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >
>> >
>> >
>> > --
>> > Guanglei Cui
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> > * Please don't post (un)subscribe requests to the list. Use the
>> > www interface or send it to gmx-users-request at gromacs.org.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Guanglei Cui
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists