[CP2K:7681] Re: CP2K compiling on CRAYXC40 - cuda version using gnu compiler

Aman Jindal amanjin... at gmail.com
Fri Apr 15 14:00:21 CEST 2016


Thank you David, I will see this arch file and will try to compile cp2k
(after modifying the file). I think I was getting this Cholesky error when
I was trying to compile cp2k first with intel compilers.
Will be back soon with more specific details.
Thank you once again,
Aman

On Thu, Apr 14, 2016 at 10:55 PM, DEC014 <dcoss... at gmail.com> wrote:

> Aman,
>
> I have received very similar errors before on Cray machines (most recently
> a few Cray XC40  and XC30 machines).  Are you getting a Cholesky Error
> along the lines of "Cholesky decompose failed: the matrix is not positive
> definite or ill-conditioned" in your output files (not the error files)?
> My problems occurred when I tried statically linking Intel MKL libraries
> for the BLAS, LAPACK, SCALAPACK, and BLACS libraries.  Even when I did not
> use the Cray cc wrapper to exclude any conflicts from Libsci_gnu_49 I was
> still getting the error.
>
> I see you are not using MKL libraries, but you might want to try a
> different version of LibSci Module.  Also, are you compiling in the Batch
> Nodes or Compute nodes?  I've had programs that misbehave when they aren't
> compiled inside the batch nodes.  To compile in a batch node, submit an
> interactive PBS job (qsub -I -A <Allocation> -q debug -l
> select=1:ncpus=24:mpiprocs=24 -l walltime=0:30:00 -N cp2k_build -j oe -j
> cp2k.oe) of course you'll have to change ncpus and mpiprocs to your Cray's
> processors.  When building inside Batch Nodes, please do not use more than
> 4 cpus for make (make -j 4).  These Batch nodes are really the PBS MOM
> nodes that dole out the PBS tasks to the compute nodes and Admins can get
> angry when you overload them.  I have attached the Architecture file that
> worked for me for my Cray XC40 build, of course this is for POPT and you'd
> have to make the necessary changes to build a Hybrid Executable.
>
> Regards,
> David
>
> On Thursday, April 14, 2016 at 5:38:10 AM UTC-4, Aman Jindal wrote:
>>
>> Yeah I did that. Now, once more I am trying to compile plumed again and
>> then cp2k (without this flag).
>> Hope it will work.
>> Thank you
>>
>> On Thu, Apr 14, 2016 at 2:53 PM, Alfio Lazzaro <alfi... at gmail.com>
>> wrote:
>>
>>> Interesting, there must something before the error you are mentioning.
>>> Have you make "clean" of CP2K before recompiling it with the flag?
>>>
>>> Alfio
>>>
>>> On Thursday, April 14, 2016 at 9:10:28 AM UTC+2, Aman Jindal wrote:
>>>>
>>>> Hello Alfio,
>>>> Thanks your valuable response. I tried compiling cp2k after removing
>>>> the flag "-mavx" , but I am getting the following error:
>>>> collect2: error: ld returned 1 exit status
>>>>
>>>> Plumed was compiled using the following commands:
>>>> 1) ./configure CXX=CC CC=cc F77=ftn F90=ftn  --prefix=/path/for/exe
>>>> --enable-mpi
>>>> 2) make
>>>> 3) make install
>>>>
>>>> Aman
>>>>
>>>>
>>>> On Wed, Apr 13, 2016 at 4:52 PM, Alfio Lazzaro <alfi... at gmail.com>
>>>> wrote:
>>>>
>>>>> Dear Aman,
>>>>> in your arch file I see that you are using "-mavx" flag. Could you
>>>>> remove it and try to recompile? Your error message says that there is
>>>>> something wrong with the flags used for the compilation (I assume the
>>>>> vector instructions), and from your last email it is seems that there is
>>>>> something wrong with PLUMED. Do you know how it was compiled?
>>>>>
>>>>> Alfio
>>>>>
>>>>>
>>>>> Il giorno mercoledì 13 aprile 2016 11:55:02 UTC+2, Aman Jindal ha
>>>>> scritto:
>>>>>>
>>>>>> Hello Samuel Andermatt,
>>>>>> I found that this error is coming only if I am compiling CP2K(version
>>>>>> 3.0)  with plumed (version 2.2.1). Because I compiled cp2k with and without
>>>>>> plumed today using CRAY-XC30-gfortran.psmp (this time without cuda) arch
>>>>>> file. Now without plumed, it is working fine, but with plumed it is giving
>>>>>> the same error (mentioned earlier).
>>>>>>
>>>>>> Do you have any idea how can I resolve this issue..
>>>>>>
>>>>>> Thank you,
>>>>>> Aman
>>>>>>
>>>>>> On Tue, Apr 12, 2016 at 6:36 PM, Aman Jindal <amanj... at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi, I used CRAY-XC30-gfortran-cuda.psmp arch file and I
>>>>>>> have gcc-5.2.0 version. Attached is the modified arch file.
>>>>>>> Thank you
>>>>>>> On Tuesday, April 12, 2016 at 6:21:25 PM UTC+5:30, Samuel Andermatt
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Which arch file did you use and which compiler version do you have?
>>>>>>>>
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