Re: [gmx-users] installation and fftw

[Omer Markovitch]

Regarding buildit FFT - I believe they say it is slower then other packages.
Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Thu, Sep 4, 2008 at 21:54, Myunggi Yi <[EMAIL PROTECTED]> wrote:

> I have done the compilation.
> Thank you so much.
>
>
>
> On Thu, Sep 4, 2008 at 12:08 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
>>
>>
>> Myunggi Yi wrote:
>>
>>> Thank you for your answer, but I can't really get you.
>>> I am using gromacs 3.3.3. .> on CentOS
>>> with AMD64 clusters with infiniband connection.
>>> I have both INTEL and GNU copilers (gcc4.1.2 and gcc3.4) and openmpi
>>> (intel and gnu).
>>> You are saying I don't have install fftw by myself, aren't you?
>>> Then how can I compile? What is the best option for the performance?
>>> I did the followings.
>>>
>>> ==
>>> ./configure --prefix=$HOME/gromacs/ --with-fft=fftw2
>>> make
>>> make install
>>>
>>> make clean
>>> ./configure --enable-mpi --disable-nice $HOME/gromacs/ --with-fft=fftw2
>>> --program-suffix=_mpi
>>> make mdrun
>>> make install-mdrun
>>> ==
>>>
>>> Is this wrong?
>>>
>>
>> Seems reasonable, did it work?
>>
>> Can I compile it with intel compiler?
>>>
>>
>> It is easy to use gcc, and definitely do *not* use gcc-4.1.2; use 3.4.
>>  There are step-by-step instructions on how to install both FFTW and Gromacs
>> on the Gromacs website:
>>
>> http://www.gromacs.org/content/view/23/33/
>>
>> Following these directly will give you the standard installation, in
>> serial and parallel, and single and double precision, if you choose.
>>
>> -Justin
>>
>>
>>> I'm sorry. I have so many questions.
>>> Please let me know how to compile it.
>>>
>>> Thank you.
>>>
>>>
>>> On Thu, Sep 4, 2008 at 11:40 AM, Roland Schulz <[EMAIL PROTECTED] >> [EMAIL PROTECTED]>> wrote:
>>>
>>>Hi,
>>>
>>>Gromacs has it's own parallel FFT which only uses FFTW for the local
>>>FFT. Thus a non-MPI FFTW is fine. and FFTW 3 is faster than 2.
>>>
>>>Roland
>>>
>>>On Thu, Sep 4, 2008 at 8:53 AM, Myunggi Yi <[EMAIL PROTECTED]
>>>> wrote:
>>>
>>>Dear gmx users,
>>>
>>>fftw3 seems doesn't support MPI.
>>>Why is the gromacs configuration default fftw3 not fftw2?
>>>Which version should I use for parallel computing?
>>>
>>>Thank you.
>>>
>>>
>>>--Best wishes,
>>>
>>>Myunggi Yi
>>>==
>>>KLB 419
>>>Institute of Molecular Biophysics
>>>Florida State University
>>>Tallahassee, FL 32306
>>>
>>>Office: (850) 645-1334
>>>http://www.scs.fsu.edu/~myunggi <
>>> http://www.scs.fsu.edu/%7Emyunggi >
>>>[EMAIL PROTECTED] 
>>>
>>>___
>>>gmx-users mailing listgmx-users@gromacs.org
>>>
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at http://www.gromacs.org/search
>>>before posting!
>>>Please don't post (un)subscribe requests to the list. Use the
>>>www interface or send it to [EMAIL PROTECTED]
>>>.
>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>>
>>>--ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>>>
>>>
>>>___
>>>gmx-users mailing listgmx-users@gromacs.org
>>>
>>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>>Please search the archive at http://www.gromacs.org/search before
>>>posting!
>>>Please don't post (un)subscribe requests to the list. Use the
>>>www interface or send it to [EMAIL PROTECTED]
>>>.
>>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>>
>>>
>>> --
>>> Best wishes,
>>>
>>> Myunggi Yi
>>> ==
>>> KLB 419
>>> Institute of Molecular Biophysics
>>> Florida State University
>>> Tallahassee, FL 32306
>>>
>>> Office: (850) 645-1334
>>> http://www.scs.fsu.edu/~myunggi
>>> [EMAIL PROTECTED] 
>>>
>>>
>>> 
>>>
>>> ___
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to [EMAIL PROTECTED]
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>> --
>> 

Re: [gmx-users] installation and fftw

[Myunggi Yi]

I have done the compilation.
Thank you so much.


On Thu, Sep 4, 2008 at 12:08 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

>
>
> Myunggi Yi wrote:
>
>> Thank you for your answer, but I can't really get you.
>> I am using gromacs 3.3.3.  on CentOS with AMD64 clusters
>> with infiniband connection.
>> I have both INTEL and GNU copilers (gcc4.1.2 and gcc3.4) and openmpi
>> (intel and gnu).
>> You are saying I don't have install fftw by myself, aren't you?
>> Then how can I compile? What is the best option for the performance?
>> I did the followings.
>>
>> ==
>> ./configure --prefix=$HOME/gromacs/ --with-fft=fftw2
>> make
>> make install
>>
>> make clean
>> ./configure --enable-mpi --disable-nice $HOME/gromacs/ --with-fft=fftw2
>> --program-suffix=_mpi
>> make mdrun
>> make install-mdrun
>> ==
>>
>> Is this wrong?
>>
>
> Seems reasonable, did it work?
>
>  Can I compile it with intel compiler?
>>
>
> It is easy to use gcc, and definitely do *not* use gcc-4.1.2; use 3.4.
>  There are step-by-step instructions on how to install both FFTW and Gromacs
> on the Gromacs website:
>
> http://www.gromacs.org/content/view/23/33/
>
> Following these directly will give you the standard installation, in serial
> and parallel, and single and double precision, if you choose.
>
> -Justin
>
>
>> I'm sorry. I have so many questions.
>> Please let me know how to compile it.
>>
>> Thank you.
>>
>>
>> On Thu, Sep 4, 2008 at 11:40 AM, Roland Schulz <[EMAIL PROTECTED] > [EMAIL PROTECTED]>> wrote:
>>
>>Hi,
>>
>>Gromacs has it's own parallel FFT which only uses FFTW for the local
>>FFT. Thus a non-MPI FFTW is fine. and FFTW 3 is faster than 2.
>>
>>Roland
>>
>>On Thu, Sep 4, 2008 at 8:53 AM, Myunggi Yi <[EMAIL PROTECTED]
>>> wrote:
>>
>>Dear gmx users,
>>
>>fftw3 seems doesn't support MPI.
>>Why is the gromacs configuration default fftw3 not fftw2?
>>Which version should I use for parallel computing?
>>
>>Thank you.
>>
>>
>>--Best wishes,
>>
>>Myunggi Yi
>>==
>>KLB 419
>>Institute of Molecular Biophysics
>>Florida State University
>>Tallahassee, FL 32306
>>
>>Office: (850) 645-1334
>>http://www.scs.fsu.edu/~myunggi<
>> http://www.scs.fsu.edu/%7Emyunggi>
>>[EMAIL PROTECTED] 
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to [EMAIL PROTECTED]
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>>--ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search before
>>posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to [EMAIL PROTECTED]
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>
>> --
>> Best wishes,
>>
>> Myunggi Yi
>> ==
>> KLB 419
>> Institute of Molecular Biophysics
>> Florida State University
>> Tallahassee, FL 32306
>>
>> Office: (850) 645-1334
>> http://www.scs.fsu.edu/~myunggi 
>> [EMAIL PROTECTED] 
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to [EMAIL PROTECTED]
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/m

Re: [gmx-users] installation and fftw

[Justin A. Lemkul]

Myunggi Yi wrote:

Thank you for your answer, but I can't really get you.
I am using gromacs 3.3.3.  on CentOS with AMD64 clusters 
with infiniband connection.
I have both INTEL and GNU copilers (gcc4.1.2 and gcc3.4) and openmpi 
(intel and gnu).

You are saying I don't have install fftw by myself, aren't you?
Then how can I compile? What is the best option for the performance?
I did the followings.

==
./configure --prefix=$HOME/gromacs/ --with-fft=fftw2
make
make install

make clean
./configure --enable-mpi --disable-nice $HOME/gromacs/ --with-fft=fftw2 
--program-suffix=_mpi

make mdrun
make install-mdrun
==

Is this wrong?


Seems reasonable, did it work?


Can I compile it with intel compiler?


It is easy to use gcc, and definitely do *not* use gcc-4.1.2; use 3.4.  There 
are step-by-step instructions on how to install both FFTW and Gromacs on the 
Gromacs website:


http://www.gromacs.org/content/view/23/33/

Following these directly will give you the standard installation, in serial and 
parallel, and single and double precision, if you choose.


-Justin



I'm sorry. I have so many questions.
Please let me know how to compile it.

Thank you.


On Thu, Sep 4, 2008 at 11:40 AM, Roland Schulz <[EMAIL PROTECTED] 
> wrote:


Hi,

Gromacs has it's own parallel FFT which only uses FFTW for the local
FFT. Thus a non-MPI FFTW is fine. and FFTW 3 is faster than 2.

Roland

On Thu, Sep 4, 2008 at 8:53 AM, Myunggi Yi <[EMAIL PROTECTED]
> wrote:

Dear gmx users,

fftw3 seems doesn't support MPI.
Why is the gromacs configuration default fftw3 not fftw2?
Which version should I use for parallel computing?

Thank you.


-- 
Best wishes,


Myunggi Yi
==
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi 
[EMAIL PROTECTED] 

___
gmx-users mailing listgmx-users@gromacs.org

http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
.
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-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov



___
gmx-users mailing listgmx-users@gromacs.org

http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php




--
Best wishes,

Myunggi Yi
==
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
[EMAIL PROTECTED] 




___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


___
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Re: [gmx-users] installation and fftw

[Myunggi Yi]

Thank you for your answer, but I can't really get you.
I am using gromacs 3.3.3. on CentOS with AMD64 clusters with infiniband
connection.
I have both INTEL and GNU copilers (gcc4.1.2 and gcc3.4) and openmpi (intel
and gnu).
You are saying I don't have install fftw by myself, aren't you?
Then how can I compile? What is the best option for the performance?
I did the followings.

==
./configure --prefix=$HOME/gromacs/ --with-fft=fftw2
make
make install

make clean
./configure --enable-mpi --disable-nice $HOME/gromacs/ --with-fft=fftw2
--program-suffix=_mpi
make mdrun
make install-mdrun
==

Is this wrong?
Can I compile it with intel compiler?

I'm sorry. I have so many questions.
Please let me know how to compile it.

Thank you.


On Thu, Sep 4, 2008 at 11:40 AM, Roland Schulz <[EMAIL PROTECTED]> wrote:

> Hi,
>
> Gromacs has it's own parallel FFT which only uses FFTW for the local FFT.
> Thus a non-MPI FFTW is fine. and FFTW 3 is faster than 2.
>
> Roland
>
> On Thu, Sep 4, 2008 at 8:53 AM, Myunggi Yi <[EMAIL PROTECTED]> wrote:
>
>> Dear gmx users,
>>
>> fftw3 seems doesn't support MPI.
>> Why is the gromacs configuration default fftw3 not fftw2?
>> Which version should I use for parallel computing?
>>
>> Thank you.
>>
>>
>> --
>> Best wishes,
>>
>> Myunggi Yi
>> ==
>> KLB 419
>> Institute of Molecular Biophysics
>> Florida State University
>> Tallahassee, FL 32306
>>
>> Office: (850) 645-1334
>> http://www.scs.fsu.edu/~myunggi 
>> [EMAIL PROTECTED]
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to [EMAIL PROTECTED]
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
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>



-- 
Best wishes,

Myunggi Yi
==
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
[EMAIL PROTECTED]
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
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Re: [gmx-users] installation and fftw

[Roland Schulz]

Hi,

Gromacs has it's own parallel FFT which only uses FFTW for the local FFT.
Thus a non-MPI FFTW is fine. and FFTW 3 is faster than 2.

Roland

On Thu, Sep 4, 2008 at 8:53 AM, Myunggi Yi <[EMAIL PROTECTED]> wrote:

> Dear gmx users,
>
> fftw3 seems doesn't support MPI.
> Why is the gromacs configuration default fftw3 not fftw2?
> Which version should I use for parallel computing?
>
> Thank you.
>
>
> --
> Best wishes,
>
> Myunggi Yi
> ==
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi 
> [EMAIL PROTECTED]
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
___
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[gmx-users] installation and fftw

[Myunggi Yi]

Dear gmx users,

fftw3 seems doesn't support MPI.
Why is the gromacs configuration default fftw3 not fftw2?
Which version should I use for parallel computing?

Thank you.


-- 
Best wishes,

Myunggi Yi
==
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
[EMAIL PROTECTED]
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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