[Llvm-bgq-discuss] more issues from trying bgclang with GROMACS

[Hal Finkel]

----- Original Message -----
> From: "Mark Abraham" <mark.abraham at scilifelab.se>
> Cc: llvm-bgq-discuss at lists.alcf.anl.gov
> Sent: Friday, February 7, 2014 8:29:18 AM
> Subject: Re: [Llvm-bgq-discuss] more issues from trying bgclang with GROMACS
> 
> 
> 
> 
> 
> Hi Hal,
> 
> AFAICS not the problem, but it's hard for a mere user to find this
> kind of stuff out:
> 
> [juqueen3 ~ (juq-homedir)] $ ls /bgsys/drivers/
> ppcfloor toolchain V1R2M0 V1R2M1

Yep; that seems good. FYI, if you run ls -l /bgsys/drivers you can see to which driver ppcfloor is symlinked, and that will give you the answer.

> 
> Jeff helpfully tried to sort me out with an ALCF account last year,
> but the cryptocard they shipped never worked with the PIN they sent
> with it, and the helpdesk insisted on me calling from Sweden to get
> any help at all, so I gave up. :-( That was about the time Congress
> decided to act more like children than usual, so maybe things were
> messier than usual! :-)

That's odd. They should be able to authenticate your identity by some mechanism other than using caller-id. :( -- When you have a chance please, try again; if they still won't help you, I'll raise the issue internally.

On the bgclang issue, if you can reasonably provide instructions on how to repeat a test showing this issue, I can try it on my end as well. More likely than not, if there is a correctness issue to debug, I'd need to do that at some point anyway.

Ah, one more thing: are you linking against anything that also links in IBM's OpenMP runtime (like ESSL SMP)? That can also cause issues like this.

 -Hal

> 
> Mark
> 
> 
> 
> 
> 
> 
> On Fri, Feb 7, 2014 at 2:27 PM, Hal Finkel < hfinkel at anl.gov > wrote:
> 
> 
> 
> ----- Original Message -----
> > From: "Mark Abraham" < mark.j.abraham at gmail.com >
> > To: llvm-bgq-discuss at lists.alcf.anl.gov
> 
> > Sent: Friday, February 7, 2014 4:55:24 AM
> > Subject: Re: [Llvm-bgq-discuss] more issues from trying bgclang
> > with GROMACS
> > 
> > 
> > 
> > Hi,
> > 
> > 
> 
> > Unfortunately, the OpenMP runs failed outright (results from
> > reduction over threads were nan, reason unclear), and there was
> > some
> > other issue. That will take some time to dig into, because we don't
> > have a "known good with bgclang" code version with which to
> > compare.
> > I'll get back to this, but it'll be a few weeks, sorry.
> 
> What driver version is the machine running? (there are known issues
> with OpenMP and driver version V1R1M2 (and earlier) -- which I did
> not think anyone was still using, but it seems some folks still
> are).
> 
> -Hal
> 
> 
> 
> > 
> > 
> > Thanks again,
> > 
> > 
> > Mark
> > 
> > 
> > 
> > On Fri, Feb 7, 2014 at 2:23 AM, Mark Abraham <
> > mark.j.abraham at gmail.com > wrote:
> > 
> > 
> > 
> > Oops, I did indeed forget to unpack that RPM. Thanks for the tip!
> > With it, the OpenMP aspect build was flawless. I was able to work
> > around the other bug by compiling those files at -O2 - which is
> > fine
> > for normal GROMACS. Test run in the queue :-)
> > 
> > 
> > Mark
> > 
> > 
> > 
> > 
> > 
> > On Fri, Feb 7, 2014 at 1:37 AM, Hal Finkel < hfinkel at anl.gov >
> > wrote:
> > 
> > 
> > 
> > ----- Original Message -----
> > > From: "Mark Abraham" < mark.j.abraham at gmail.com >
> > > To: llvm-bgq-discuss at lists.alcf.anl.gov
> > > Sent: Thursday, February 6, 2014 6:26:55 PM
> > > Subject: [Llvm-bgq-discuss] more issues from trying bgclang with
> > > GROMACS
> > > 
> > > 
> > > 
> > > Hi,
> > > 
> > > 
> > > I had another go compiling GROMACS 5.0 beta with bgclang latest
> > > RPM
> > > (r200401-20140129). CMake detection of OpenMP support in mpiclang
> > > failed. Detection should just work because using the -fopenmp
> > > flag
> > > is a standard way to do it. When I tried a manual compile:
> > > 
> > > 
> > > 
> > > $ ~/progs/bgclang/current/bin/bgclang -fopenmp test.c -o test
> > > /homea/slbio/slbio013/progs/bgclang/r200401-20140129/binutils/bin/ld:
> > > cannot find -liomp5
> > > clang: error: linker command failed with exit code 1 (use -v to
> > > see
> > > invocation)
> > > 
> > > 
> > > That looks like a lingering Intel-ism?
> > 
> > Yes, but that's okay, the libomp package should create the
> > necessary
> > symlink for you. Did you install
> > bgclang-libomp-r200401-20140129-1-1.ppc64.rpm?
> > 
> > -Hal
> > 
> > 
> > > 
> > > 
> > > The MPI plus non-OpenMP build seemed to go OK, but a file in our
> > > bundled lapack subset provoked a bug (attached in tarball). That
> > > file was not a problem in ~August 2013.
> > > 
> > > 
> > > Thanks again for the effort!
> > > 
> > > 
> > > Cheers,
> > > 
> > > 
> > > Mark
> > > _______________________________________________
> > > llvm-bgq-discuss mailing list
> > > llvm-bgq-discuss at lists.alcf.anl.gov
> > > https://lists.alcf.anl.gov/mailman/listinfo/llvm-bgq-discuss
> > > 
> > 
> > --
> > Hal Finkel
> > Assistant Computational Scientist
> > Leadership Computing Facility
> > Argonne National Laboratory
> > 
> > 
> > 
> > _______________________________________________
> > llvm-bgq-discuss mailing list
> > llvm-bgq-discuss at lists.alcf.anl.gov
> > https://lists.alcf.anl.gov/mailman/listinfo/llvm-bgq-discuss
> > 
> 
> --
> Hal Finkel
> Assistant Computational Scientist
> Leadership Computing Facility
> Argonne National Laboratory
> _______________________________________________
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> llvm-bgq-discuss at lists.alcf.anl.gov
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> 
> 
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-- 
Hal Finkel
Assistant Computational Scientist
Leadership Computing Facility
Argonne National Laboratory