Re: [easybuild] GROMACS with gpu support

2017-03-01 Thread Åke Sandgren 
And now updated to include the patches...

On 03/01/2017 09:26 PM, Åke Sandgren wrote:
> PR 4232, please take a look
> 
> On 03/01/2017 08:56 PM, Siddiqui, Shahzeb wrote:
>> Please fire away!
>>
>> -Original Message-
>> From: easybuild-requ...@lists.ugent.be 
>> [mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Åke Sandgren
>> Sent: Wednesday, March 1, 2017 2:54 PM
>> To: easybuild@lists.ugent.be
>> Cc: Oliver Stueker
>> Subject: Re: [easybuild] GROMACS with gpu support
>>
>> I have a easyconfig for GROMACS 2016 with the goolfc toolchain (CUDA)
>>
>> I keep forgetting to PR it.
>>
>> It's been in production for a couple of month now.
>>
>> Do you want me to PR it?
>>
>> On 03/01/2017 08:47 PM, Vanzo, Davide wrote:
>>> Maxime and Oliver,
>>> since GROMACS with GPU acceleration is in my software list for the 
>>> fosscuda toolchain I will be working on, I would be interested in 
>>> sharing the pain if somebody is already working on it.
>>>
>>> --
>>> Davide Vanzo, PhD
>>> Application Developer
>>> Adjunct Assistant Professor of Chemical and Biomolecular Engineering 
>>> Advanced Computing Center for Research and Education (ACCRE) 
>>> Vanderbilt University - Hill Center 201
>>> (615)-875-9137
>>> www.accre.vanderbilt.edu
>>>
>>> On Mar 1 2017, at 1:43 pm, Maxime Boissonneault 
>>>  wrote:
>>>
>>> Hi Shahzeb,
>>> I am putting you in contact with my colleague Oliver Stueker. He is
>>> actually working to modify the recipe for GROMACS GPU. Maybe he can
>>> help.
>>>
>>> Maxime
>>>
>>> On 17-03-01 14:38, Siddiqui, Shahzeb wrote:
 g
 Hello,

  

 I am curious how I would build GROMACS with GPU support, I only
 see GROMACS build with multithreaded and hybrid approach. I notice
 this is just a tweak to toolchainopts that sets whether to build
 with openmp and mpi. This seems fine, but not sure how I would
 build with cuda.

  

 Do I need to load a cuda specific toolchain like gompic or intelcuda.

  

 Regards,

  

  

  

 Shahzeb Siddiqui

 HPC Linux Engineer

 B2220-447.2

 Groton, CT

  

>>>
>>
>> --
>> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
>> Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
>> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
>>
> 

-- 
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se

Re: [easybuild] GROMACS with gpu support

2017-03-01 Thread Åke Sandgren 
PR 4232, please take a look

On 03/01/2017 08:56 PM, Siddiqui, Shahzeb wrote:
> Please fire away!
> 
> -Original Message-
> From: easybuild-requ...@lists.ugent.be 
> [mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Åke Sandgren
> Sent: Wednesday, March 1, 2017 2:54 PM
> To: easybuild@lists.ugent.be
> Cc: Oliver Stueker
> Subject: Re: [easybuild] GROMACS with gpu support
> 
> I have a easyconfig for GROMACS 2016 with the goolfc toolchain (CUDA)
> 
> I keep forgetting to PR it.
> 
> It's been in production for a couple of month now.
> 
> Do you want me to PR it?
> 
> On 03/01/2017 08:47 PM, Vanzo, Davide wrote:
>> Maxime and Oliver,
>> since GROMACS with GPU acceleration is in my software list for the 
>> fosscuda toolchain I will be working on, I would be interested in 
>> sharing the pain if somebody is already working on it.
>>
>> --
>> Davide Vanzo, PhD
>> Application Developer
>> Adjunct Assistant Professor of Chemical and Biomolecular Engineering 
>> Advanced Computing Center for Research and Education (ACCRE) 
>> Vanderbilt University - Hill Center 201
>> (615)-875-9137
>> www.accre.vanderbilt.edu
>>
>> On Mar 1 2017, at 1:43 pm, Maxime Boissonneault 
>>  wrote:
>>
>> Hi Shahzeb,
>> I am putting you in contact with my colleague Oliver Stueker. He is
>> actually working to modify the recipe for GROMACS GPU. Maybe he can
>> help.
>>
>> Maxime
>>
>> On 17-03-01 14:38, Siddiqui, Shahzeb wrote:
>>> g
>>> Hello,
>>>
>>>  
>>>
>>> I am curious how I would build GROMACS with GPU support, I only
>>> see GROMACS build with multithreaded and hybrid approach. I notice
>>> this is just a tweak to toolchainopts that sets whether to build
>>> with openmp and mpi. This seems fine, but not sure how I would
>>> build with cuda.
>>>
>>>  
>>>
>>> Do I need to load a cuda specific toolchain like gompic or intelcuda.
>>>
>>>  
>>>
>>> Regards,
>>>
>>>  
>>>
>>>  
>>>
>>>  
>>>
>>> Shahzeb Siddiqui
>>>
>>> HPC Linux Engineer
>>>
>>> B2220-447.2
>>>
>>> Groton, CT
>>>
>>>  
>>>
>>
> 
> --
> Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
> Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
> Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
> 

-- 
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se

Re: [easybuild] GROMACS with gpu support

2017-03-01 Thread Vanzo, Davide 
Shahzeb,
the fosscuda toolchain is still a work in progress and no PR have been released 
yet.
Hopefully I will get something working in the next months.

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu


On Mar 1 2017, at 2:00 pm, Siddiqui, Shahzeb  
wrote:

This might be a dumb question, I don’t see a foss toolchain, the only closest 
one is goolfc which uses gompic toolchain. Which toolchain should we use?



From: easybuild-requ...@lists.ugent.be 
[mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Vanzo, Davide
Sent: Wednesday, March 1, 2017 2:48 PM
To: easybuild@lists.ugent.be
Cc: Oliver Stueker
Subject: Re: [easybuild] GROMACS with gpu support



Maxime and Oliver,

since GROMACS with GPU acceleration is in my software list for the fosscuda 
toolchain I will be working on, I would be interested in sharing the pain if 
somebody is already working on it.

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu

[https://link.nylas.com/open/6n4bjcakifea4azkemwwns1da/local-37bc18e0-2b36]

On Mar 1 2017, at 1:43 pm, Maxime Boissonneault 
>
 wrote:

Hi Shahzeb,
I am putting you in contact with my colleague Oliver Stueker. He is actually 
working to modify the recipe for GROMACS GPU. Maybe he can help.

Maxime

On 17-03-01 14:38, Siddiqui, Shahzeb wrote:

Hello,



I am curious how I would build GROMACS with GPU support, I only see GROMACS 
build with multithreaded and hybrid approach. I notice this is just a tweak to 
toolchainopts that sets whether to build with openmp and mpi. This seems fine, 
but not sure how I would build with cuda.



Do I need to load a cuda specific toolchain like gompic or intelcuda.



Regards,







Shahzeb Siddiqui

HPC Linux Engineer

B2220-447.2

Groton, CT

RE: [easybuild] GROMACS with gpu support

2017-03-01 Thread Siddiqui, Shahzeb 
This might be a dumb question, I don’t see a foss toolchain, the only closest 
one is goolfc which uses gompic toolchain. Which toolchain should we use?

From: easybuild-requ...@lists.ugent.be 
[mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Vanzo, Davide
Sent: Wednesday, March 1, 2017 2:48 PM
To: easybuild@lists.ugent.be
Cc: Oliver Stueker
Subject: Re: [easybuild] GROMACS with gpu support

Maxime and Oliver,
since GROMACS with GPU acceleration is in my software list for the fosscuda 
toolchain I will be working on, I would be interested in sharing the pain if 
somebody is already working on it.

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu
[https://link.nylas.com/open/6n4bjcakifea4azkemwwns1da/local-37bc18e0-2b36]

On Mar 1 2017, at 1:43 pm, Maxime Boissonneault 
>
 wrote:
Hi Shahzeb,
I am putting you in contact with my colleague Oliver Stueker. He is actually 
working to modify the recipe for GROMACS GPU. Maybe he can help.

Maxime

On 17-03-01 14:38, Siddiqui, Shahzeb wrote:

Hello,



I am curious how I would build GROMACS with GPU support, I only see GROMACS 
build with multithreaded and hybrid approach. I notice this is just a tweak to 
toolchainopts that sets whether to build with openmp and mpi. This seems fine, 
but not sure how I would build with cuda.



Do I need to load a cuda specific toolchain like gompic or intelcuda.



Regards,







Shahzeb Siddiqui

HPC Linux Engineer

B2220-447.2

Groton, CT

RE: [easybuild] GROMACS with gpu support

2017-03-01 Thread Siddiqui, Shahzeb 
Please fire away!

-Original Message-
From: easybuild-requ...@lists.ugent.be 
[mailto:easybuild-requ...@lists.ugent.be] On Behalf Of Åke Sandgren
Sent: Wednesday, March 1, 2017 2:54 PM
To: easybuild@lists.ugent.be
Cc: Oliver Stueker
Subject: Re: [easybuild] GROMACS with gpu support

I have a easyconfig for GROMACS 2016 with the goolfc toolchain (CUDA)

I keep forgetting to PR it.

It's been in production for a couple of month now.

Do you want me to PR it?

On 03/01/2017 08:47 PM, Vanzo, Davide wrote:
> Maxime and Oliver,
> since GROMACS with GPU acceleration is in my software list for the 
> fosscuda toolchain I will be working on, I would be interested in 
> sharing the pain if somebody is already working on it.
> 
> --
> Davide Vanzo, PhD
> Application Developer
> Adjunct Assistant Professor of Chemical and Biomolecular Engineering 
> Advanced Computing Center for Research and Education (ACCRE) 
> Vanderbilt University - Hill Center 201
> (615)-875-9137
> www.accre.vanderbilt.edu
> 
> On Mar 1 2017, at 1:43 pm, Maxime Boissonneault 
>  wrote:
> 
> Hi Shahzeb,
> I am putting you in contact with my colleague Oliver Stueker. He is
> actually working to modify the recipe for GROMACS GPU. Maybe he can
> help.
> 
> Maxime
> 
> On 17-03-01 14:38, Siddiqui, Shahzeb wrote:
>>g
>> Hello,
>>
>>  
>>
>> I am curious how I would build GROMACS with GPU support, I only
>> see GROMACS build with multithreaded and hybrid approach. I notice
>> this is just a tweak to toolchainopts that sets whether to build
>> with openmp and mpi. This seems fine, but not sure how I would
>> build with cuda.
>>
>>  
>>
>> Do I need to load a cuda specific toolchain like gompic or intelcuda.
>>
>>  
>>
>> Regards,
>>
>>  
>>
>>  
>>
>>  
>>
>> Shahzeb Siddiqui
>>
>> HPC Linux Engineer
>>
>> B2220-447.2
>>
>> Groton, CT
>>
>>  
>>
> 

--
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se

Re: [easybuild] GROMACS with gpu support

2017-03-01 Thread Åke Sandgren 
I have a easyconfig for GROMACS 2016 with the goolfc toolchain (CUDA)

I keep forgetting to PR it.

It's been in production for a couple of month now.

Do you want me to PR it?

On 03/01/2017 08:47 PM, Vanzo, Davide wrote:
> Maxime and Oliver,
> since GROMACS with GPU acceleration is in my software list for the
> fosscuda toolchain I will be working on, I would be interested in
> sharing the pain if somebody is already working on it.
> 
> -- 
> Davide Vanzo, PhD
> Application Developer
> Adjunct Assistant Professor of Chemical and Biomolecular Engineering
> Advanced Computing Center for Research and Education (ACCRE)
> Vanderbilt University - Hill Center 201
> (615)-875-9137
> www.accre.vanderbilt.edu
> 
> On Mar 1 2017, at 1:43 pm, Maxime Boissonneault
>  wrote:
> 
> Hi Shahzeb,
> I am putting you in contact with my colleague Oliver Stueker. He is
> actually working to modify the recipe for GROMACS GPU. Maybe he can
> help.
> 
> Maxime
> 
> On 17-03-01 14:38, Siddiqui, Shahzeb wrote:
>>g
>> Hello,
>>
>>  
>>
>> I am curious how I would build GROMACS with GPU support, I only
>> see GROMACS build with multithreaded and hybrid approach. I notice
>> this is just a tweak to toolchainopts that sets whether to build
>> with openmp and mpi. This seems fine, but not sure how I would
>> build with cuda.
>>
>>  
>>
>> Do I need to load a cuda specific toolchain like gompic or intelcuda.
>>
>>  
>>
>> Regards,
>>
>>  
>>
>>  
>>
>>  
>>
>> Shahzeb Siddiqui
>>
>> HPC Linux Engineer
>>
>> B2220-447.2
>>
>> Groton, CT
>>
>>  
>>
> 

-- 
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90-580 14
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se

Re: [easybuild] GROMACS with gpu support

2017-03-01 Thread Vanzo, Davide 
Maxime and Oliver,
since GROMACS with GPU acceleration is in my software list for the fosscuda 
toolchain I will be working on, I would be interested in sharing the pain if 
somebody is already working on it.

--
Davide Vanzo, PhD
Application Developer
Adjunct Assistant Professor of Chemical and Biomolecular Engineering
Advanced Computing Center for Research and Education (ACCRE)
Vanderbilt University - Hill Center 201
(615)-875-9137
www.accre.vanderbilt.edu


On Mar 1 2017, at 1:43 pm, Maxime Boissonneault 
 wrote:
Hi Shahzeb,
I am putting you in contact with my colleague Oliver Stueker. He is actually 
working to modify the recipe for GROMACS GPU. Maybe he can help.

Maxime

On 17-03-01 14:38, Siddiqui, Shahzeb wrote:

Hello,



I am curious how I would build GROMACS with GPU support, I only see GROMACS 
build with multithreaded and hybrid approach. I notice this is just a tweak to 
toolchainopts that sets whether to build with openmp and mpi. This seems fine, 
but not sure how I would build with cuda.



Do I need to load a cuda specific toolchain like gompic or intelcuda.



Regards,







Shahzeb Siddiqui

HPC Linux Engineer

B2220-447.2

Groton, CT

Re: [easybuild] GROMACS with gpu support

2017-03-01 Thread Maxime Boissonneault 

Hi Shahzeb,
I am putting you in contact with my colleague Oliver Stueker. He is 
actually working to modify the recipe for GROMACS GPU. Maybe he can help.


Maxime

On 17-03-01 14:38, Siddiqui, Shahzeb wrote:


Hello,

I am curious how I would build GROMACS with GPU support, I only see 
GROMACS build with multithreaded and hybrid approach. I notice this is 
just a tweak to toolchainopts that sets whether to build with openmp 
and mpi. This seems fine, but not sure how I would build with cuda.


Do I need to load a cuda specific toolchain like gompic or intelcuda.

Regards,

Shahzeb Siddiqui

HPC Linux Engineer

B2220-447.2

Groton, CT

[easybuild] GROMACS with gpu support

2017-03-01 Thread Siddiqui, Shahzeb 
Hello,

I am curious how I would build GROMACS with GPU support, I only see GROMACS 
build with multithreaded and hybrid approach. I notice this is just a tweak to 
toolchainopts that sets whether to build with openmp and mpi. This seems fine, 
but not sure how I would build with cuda.

Do I need to load a cuda specific toolchain like gompic or intelcuda.

Regards,



Shahzeb Siddiqui
HPC Linux Engineer
B2220-447.2
Groton, CT

Re: [easybuild] next EasyBuild conf call: Wed Mar 1st 2017, 5pm CET

2017-03-01 Thread Kenneth Hoste 
notes are available at 
https://github.com/hpcugent/easybuild/wiki/Conference-call-notes-20170301


next conf call is planned for Wed March 15th, see also 
https://plus.google.com/events/c1f3gt69hoashfluir48htdsols


On 28/02/2017 20:00, Kenneth Hoste wrote:

Dear EasyBuilders,

The next EasyBuild conf call is planned for Wednesday March 1st 2017, 
5pm CET;

see also https://plus.google.com/events/ce5mo25p4i06kcbsk9tqjhg4tns .

Current agenda:

  * outlook to EasyBuild v3.1.1 (bugfix/update release)
  * support allowing to run EasyBuild as root?
  * Python/R/Perl easyconfigs (& more) for 2017a toolchains
  * Q

Suggestions for additional topics are welcome.
Please let us know if you're planning to attend this conf call.

More information about the EasyBuild conf calls is available at 
https://github.com/hpcugent/easybuild/wiki/Conference-calls .



regards,

Kenneth

Re: [easybuild] What does "pic:True" do for a toolchain ?

2017-03-01 Thread Maxime Boissonneault 

Thanks Alan,
This explains that. We'll look into using the gcc/system toolchain.

Maxime

On 17-03-01 09:59, Alan O'Cais wrote:
Afraid so, the toolchainopts do nothing for the dummy toolchain since 
EasyBuild doesn't "know" anything about the options dummy an accept.


If you want to wrap the system compiler properly, you should probable 
use GCC/system (see 
https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/g/GCC/GCC-system.eb)

[easybuild] What does "pic:True" do for a toolchain ?

2017-03-01 Thread Maxime Boissonneault 

Hi,

What does "pic:True" do for a toolchain ?

I would have expected it to enable -fPIC and -DPIC flags. However, I 
just tried installing JasPer-1.900.1 with the dummy-dummy toolchain, and 
the flags were not there (and a futher build of GDAL failed because the 
symbols did not have PIC).


I discovered that only when adding --enable-shared to the configopts 
were the flags actually added (I suspect by the configure, rather than 
by EasyBuild).



Is this expected ?

--
-
Maxime Boissonneault
Analyste de calcul - Calcul Québec, Université Laval
Président - Comité de coordination du soutien à la recherche de Calcul Québec
Team lead - Research Support National Team, Compute Canada
Instructeur Software Carpentry
Ph. D. en physique