subject:"\[gmx\-users\] CMake Error at cmake\/gmxManageSimd.cmake\:67 \(message\)\: Found a compiler flag for AVX2 support, but some other problem exists."

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-05 Thread Atila Petrosian

Dear Justin,

Thanks for your answers and helps.

My mdrun was finished.

> If you want specific help about why you're observing some given
> speed/performance, you need to provide actual details about the simulated
> system, hardware, etc. and upload full .log files to a file-sharing
service
> (e.g. pastebin) and provide a URL.

Details about the simulated system:

A protein with 54 residues, 4214 water molecule and 7 Cl ions, totally
13599 atoms.

Details about the hardware:

CPU: Intel Corei7 6900K
Mainboard:Asus X99E ws
RAM: 4*8 GB 2400, DDR4
VGA: GTX 1080 EVGA
HDD: 1TB SATA3 Seagate
SSD: 240GB

The log file (npt.log) is obtained from the following link:

https://www.dropbox.com/s/85tcj99tdhbjs41/npt.log?dl=0

Please guide me to obtain maximum efficiency from run on gpu.

Best,
Atila
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Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Justin Lemkul




On 9/4/16 2:52 PM, Atila Petrosian wrote:

Dear Justin,

Thanks for your good guidance (There is only one program now.).

My previous problem was solved.

Now, I have another question.

I used two times following commands for my system (protein):

gmx_mpi mdrun -v -deffnm  npt >& npt_1.job &

gmx_mpi mdrun -nb gpu -v -deffnm  npt >& npt_2.job &

In both cases, run will finish Mon Sep  5 06:33:19 2016 (same time).

Run on gpu should faster than that on cpu. Why is not it for me?

How to find mdrun run on gpu or cpu?



The default for the -nb option is "auto" so if there is a GPU, mdrun will find 
it and use it.  So probably both of your runs are doing the same thing.  Of 
course, reading the .log file will tell you exactly what mdrun is doing and why 
it is doing it.


Also relevant is 
http://www.gromacs.org/Documentation/Acceleration_and_parallelization


If you want specific help about why you're observing some given 
speed/performance, you need to provide actual details about the simulated 
system, hardware, etc. and upload full .log files to a file-sharing service 
(e.g. pastebin) and provide a URL.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian

Dear Justin,

Thanks for your good guidance (There is only one program now.).

My previous problem was solved.

Now, I have another question.

I used two times following commands for my system (protein):

gmx_mpi mdrun -v -deffnm  npt >& npt_1.job &

gmx_mpi mdrun -nb gpu -v -deffnm  npt >& npt_2.job &

In both cases, run will finish Mon Sep  5 06:33:19 2016 (same time).

Run on gpu should faster than that on cpu. Why is not it for me?

How to find mdrun run on gpu or cpu?

Best,

Atila
-- 
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Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Justin Lemkul




On 9/4/16 1:45 PM, Atila Petrosian wrote:

Dear Mark,

In /usr/local/gromasc/bin directory, there are only

demux.pl
gmx-completion.bash
gmx-completion-gmx_mpi.bash
gmx_mpi
GMXRC
GMXRC.bash
GMXRC.csh
GMXRC.zshxplor2gmx.pl

In this directory, there is gmx_mpi rather than gmx. It is true based
on the 
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/removed-features.html#removed-temporary-symlinks-from-pre-5-0-tool-names

In above link:

That period is now over, so gmx tool (or gmx_mpi tool) is the only way
to use GROMACS in 5.1. The mdrun-only build will build mdrun (or
mdrun_mpi as appropriate).

But there are not any tool in /usr/local/gromacs/bin directory

Are you sure the lack of tools such as pdb2gmx, editconf, mdrun,
grompp and  is not a problem ???



This is not a problem.

There is only one program now.  It is called gmx, or gmx_mpi if you enabled MPI. 
 Everything is now a module of the gmx program.


gmx pdb2gmx...
gmx grompp...

etc.

There are important changes to several tools, including re-naming and very 
different syntax.  Again, there is lots of documentation, mailing list 
discussion, and tutorial updates that are relevant here.


-Justin


I am confused. Please tell me hoe to use gromacs 5.1 tools.


Best,

Atila



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian

Dear Mark,

In /usr/local/gromasc/bin directory, there are only

demux.pl
gmx-completion.bash
gmx-completion-gmx_mpi.bash
gmx_mpi
GMXRC
GMXRC.bash
GMXRC.csh
GMXRC.zshxplor2gmx.pl

In this directory, there is gmx_mpi rather than gmx. It is true based
on the 
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/removed-features.html#removed-temporary-symlinks-from-pre-5-0-tool-names

In above link:

That period is now over, so gmx tool (or gmx_mpi tool) is the only way
to use GROMACS in 5.1. The mdrun-only build will build mdrun (or
mdrun_mpi as appropriate).

But there are not any tool in /usr/local/gromacs/bin directory

Are you sure the lack of tools such as pdb2gmx, editconf, mdrun,
grompp and  is not a problem ???

I am confused. Please tell me hoe to use gromacs 5.1 tools.


Best,

Atila
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[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian

Dear Mark,

> you still need to source the GMXRC from the version you want to use > > in 
> the terminal you want to use it from.

I used source /usr/local/gromacs/bin/GMXRC,

But, when I use gmx pdb2gmx command, I encountered with:

-bash: gmx: command not found

Best,
Atila
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Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Mark Abraham

Hi,

Like the installation instructions say, you still need to source the GMXRC
from the version you want to use in the terminal you want to use it from.

Mark

On Sun, 4 Sep 2016 16:02 Atila Petrosian  wrote:

> Dear Justin,
>
> Thanks for your answer.
>
> I know several programs have been renamed in new version such as
> pdb2gmx --> gmx pdb2gmx. But when I use gmx pdb2gmx,
>
> -bash: gmx: command not found
>
> Best,
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian

Dear Justin,

Thanks for your answer.

I know several programs have been renamed in new version such as
pdb2gmx --> gmx pdb2gmx. But when I use gmx pdb2gmx,

-bash: gmx: command not found

Best,
-- 
Gromacs Users mailing list

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Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Justin Lemkul

On Sunday, September 4, 2016, Atila Petrosian 
wrote:

> Dear Mark,
>
> Thanks for your quick answer.
>
> Now, how to use gromacs 5.1.3 commands?
>
> The reason of my question:
>
> There is gromacs 4.5.4 (in /opt/bio directory) in my Rocks cluster system
> by default.
>
> I used source /usr/local/gromacs/bin/GMXRC,
>
> then
>
> pdb2gmx
>
> Unfortunately, pdb2gmx related to gromacs 4.5.4 is run.
>
> Please guide me to resolve this issue.
>
>
The syntax since version 5.0 is different. Please read the documentation
and tutorials for the new version. Several programs have been renamed, as
well.

-Justin

> Best,
> Atila
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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> send a mail to gmx-users-requ...@gromacs.org .
>

-- 

==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian

Dear Mark,

Thanks for your quick answer.

Now, how to use gromacs 5.1.3 commands?

The reason of my question:

There is gromacs 4.5.4 (in /opt/bio directory) in my Rocks cluster system
by default.

I used source /usr/local/gromacs/bin/GMXRC,

then

pdb2gmx

Unfortunately, pdb2gmx related to gromacs 4.5.4 is run.

Please guide me to resolve this issue.

Best,
Atila
-- 
Gromacs Users mailing list

* Please search the archive at 
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Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Mark Abraham

Hi,

Yes.
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/removed-features.html#removed-temporary-symlinks-from-pre-5-0-tool-names

Mark

On Sun, Sep 4, 2016 at 3:19 PM Atila Petrosian 
wrote:

> Dear Mark,
>
> Thanks for the guidance.
>
> I updated gcc using your proposed link (https://ed.braaten.net/blog/
> 2014-05-28-devtools-for-centos/
> ).
>
> Now my Rocks cluster system has following info:
>
> Rocks 6.2
> CentOS 6.6
> Cuda 7.5 and 8 (/usr/local/cuda)
> gcc 4.8.2
>
> I installed gromacs 5.1.3 based on following link:  gromacs
> http://manual.gromacs.org/documentation/5.1.3/dev-manual/testutils.html
>
> I used the following commands:
>
> cd gromacs-5.1.3
> mkdir build
> cd build
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
> -DGMX_GPU=ON
> make
> make check
> make install
> source /usr/local/gromacs/bin/GMXRC
>
> *There is no error in above command.*
>
> Thera are following files in /usr/local/gromacs/bin directory:
>
> demux.pl
> gmx-completion.bash
> gmx-completion-gmx_mpi.bash
> gmx_mpi
> GMXRC
> GMXRC.bash
> GMXRC.csh
> GMXRC.zsh
> xplor2gmx.pl
>
> Is my gromacs installation on GPU true?
>
> The reason of my question is that when I had installed gromacs 5.0.5 as
> parallel (-DGMX_MPI=ON) on another Rocks system, there were following files
> in /usr/local/gromacs/bin directory:
>
> demux.pl
> do_dssp -> gmx
> editconf -> gmx
> eneconv -> gmx
> g_anadock -> gmx
> g_anaeig -> gmx
> g_analyze -> gmx
> g_angle -> gmx
> g_bar -> gmx
> g_bond -> gmx
> g_bundle -> gmx
> g_chi -> gmx
> g_cluster -> gmx
> g_clustsize -> gmx
> g_confrms -> gmx
> g_covar -> gmx
> g_current -> gmx
> g_density -> gmx
> g_densmap -> gmx
> g_densorder -> gmx
> g_dielectric -> gmx
> g_dipoles -> gmx
> g_disre -> gmx
> g_dist -> gmx
> g_dos -> gmx
> g_dyecoupl -> gmx
> g_dyndom -> gmx
> genbox -> gmx
> genconf -> gmx
> g_enemat -> gmx
> g_energy -> gmx
> genion -> gmx
> genrestr -> gmx
> g_filter -> gmx
> g_gyrate -> gmx
> g_h2order -> gmx
> g_hbond -> gmx
> g_helix -> gmx
> g_helixorient -> gmx
> g_hydorder -> gmx
> g_lie -> gmx
> g_mdmat -> gmx
> g_mindist -> gmx
> g_morph -> gmx
> g_msd -> gmx
> gmx
> gmxcheck -> gmx
> gmx-completion.bash
> gmx-completion-gmx.bash
> gmx-completion-gmx_mpi.bash
> gmxdump -> gmx
> gmx_mpi
> GMXRC
> GMXRC.bash
> GMXRC.csh
> GMXRC.zsh
> g_nmeig -> gmx
> g_nmens -> gmx
> g_nmtraj -> gmx
> g_options -> gmx
> g_order -> gmx
> g_pme_error -> gmx
> g_polystat -> gmx
> g_potential -> gmx
> g_principal -> gmx
> g_protonate -> gmx
> g_rama -> gmx
> g_rdf -> gmx
> g_rms -> gmx
> g_rmsdist -> gmx
> g_rmsf -> gmx
> grompp -> gmx
> g_rotacf -> gmx
> g_rotmat -> gmx
> g_saltbr -> gmx
> g_sans -> gmx
> g_sas -> gmx
> g_saxs -> gmx
> g_select -> gmx
> g_sgangle -> gmx
> g_sham -> gmx
> g_sigeps -> gmx
> g_sorient -> gmx
> g_spatial -> gmx
> g_spol -> gmx
> g_tcaf -> gmx
> g_traj -> gmx
> g_tune_pme -> gmx
> g_vanhove -> gmx
> g_velacc -> gmx
> g_wham -> gmx
> g_wheel -> gmx
> g_x2top -> gmx
> make_edi -> gmx
> make_ndx -> gmx
> md.log
> mdrun -> gmx
> mk_angndx -> gmx
> pdb2gmx -> gmx
> tpbconv -> gmx
> trjcat -> gmx
> trjconv -> gmx
> trjorder -> gmx
> xplor2gmx.pl
> xpm2ps -> gmx
>
> My main goal is to install gromacs on gpu.
>
> Please guide me.
>
> Best,
> Atila
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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>
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[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-04 Thread Atila Petrosian

Dear Mark,

Thanks for the guidance.

I updated gcc using your proposed link (https://ed.braaten.net/blog/
2014-05-28-devtools-for-centos/).

Now my Rocks cluster system has following info:

Rocks 6.2
CentOS 6.6
Cuda 7.5 and 8 (/usr/local/cuda)
gcc 4.8.2

I installed gromacs 5.1.3 based on following link:  gromacs
http://manual.gromacs.org/documentation/5.1.3/dev-manual/testutils.html

I used the following commands:

cd gromacs-5.1.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
-DGMX_GPU=ON
make
make check
make install
source /usr/local/gromacs/bin/GMXRC

*There is no error in above command.*

Thera are following files in /usr/local/gromacs/bin directory:

demux.pl
gmx-completion.bash
gmx-completion-gmx_mpi.bash
gmx_mpi
GMXRC
GMXRC.bash
GMXRC.csh
GMXRC.zsh
xplor2gmx.pl

Is my gromacs installation on GPU true?

The reason of my question is that when I had installed gromacs 5.0.5 as
parallel (-DGMX_MPI=ON) on another Rocks system, there were following files
in /usr/local/gromacs/bin directory:

demux.pl
do_dssp -> gmx
editconf -> gmx
eneconv -> gmx
g_anadock -> gmx
g_anaeig -> gmx
g_analyze -> gmx
g_angle -> gmx
g_bar -> gmx
g_bond -> gmx
g_bundle -> gmx
g_chi -> gmx
g_cluster -> gmx
g_clustsize -> gmx
g_confrms -> gmx
g_covar -> gmx
g_current -> gmx
g_density -> gmx
g_densmap -> gmx
g_densorder -> gmx
g_dielectric -> gmx
g_dipoles -> gmx
g_disre -> gmx
g_dist -> gmx
g_dos -> gmx
g_dyecoupl -> gmx
g_dyndom -> gmx
genbox -> gmx
genconf -> gmx
g_enemat -> gmx
g_energy -> gmx
genion -> gmx
genrestr -> gmx
g_filter -> gmx
g_gyrate -> gmx
g_h2order -> gmx
g_hbond -> gmx
g_helix -> gmx
g_helixorient -> gmx
g_hydorder -> gmx
g_lie -> gmx
g_mdmat -> gmx
g_mindist -> gmx
g_morph -> gmx
g_msd -> gmx
gmx
gmxcheck -> gmx
gmx-completion.bash
gmx-completion-gmx.bash
gmx-completion-gmx_mpi.bash
gmxdump -> gmx
gmx_mpi
GMXRC
GMXRC.bash
GMXRC.csh
GMXRC.zsh
g_nmeig -> gmx
g_nmens -> gmx
g_nmtraj -> gmx
g_options -> gmx
g_order -> gmx
g_pme_error -> gmx
g_polystat -> gmx
g_potential -> gmx
g_principal -> gmx
g_protonate -> gmx
g_rama -> gmx
g_rdf -> gmx
g_rms -> gmx
g_rmsdist -> gmx
g_rmsf -> gmx
grompp -> gmx
g_rotacf -> gmx
g_rotmat -> gmx
g_saltbr -> gmx
g_sans -> gmx
g_sas -> gmx
g_saxs -> gmx
g_select -> gmx
g_sgangle -> gmx
g_sham -> gmx
g_sigeps -> gmx
g_sorient -> gmx
g_spatial -> gmx
g_spol -> gmx
g_tcaf -> gmx
g_traj -> gmx
g_tune_pme -> gmx
g_vanhove -> gmx
g_velacc -> gmx
g_wham -> gmx
g_wheel -> gmx
g_x2top -> gmx
make_edi -> gmx
make_ndx -> gmx
md.log
mdrun -> gmx
mk_angndx -> gmx
pdb2gmx -> gmx
tpbconv -> gmx
trjcat -> gmx
trjconv -> gmx
trjorder -> gmx
xplor2gmx.pl
xpm2ps -> gmx

My main goal is to install gromacs on gpu.

Please guide me.

Best,
Atila
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Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-03 Thread Mark Abraham

Hi,

As the message says, you should update your binutils package. Using such
distros based on old OS infrastructure with new hardware guarantees you
have to update various things in order to benefit from your expensive
hardware. In your case,
https://ed.braaten.net/blog/2014-05-28-devtools-for-centos/ or maybe
devtoolset-3 is appropriate. This will be absolutely necessary for GROMACS
2016 and up.

Mark

On Sat, 3 Sep 2016 13:10 Atila Petrosian  wrote:

> Dear gromacs users,
>
> I am using Rocks cluster system with following info:
>
> Rocks 6.2
> CentOS 6.6
> Cuda 7.5 and 8
> gcc 4.4.7
>
> I am installing gromacs-5.1.3. I used following command:
>
> cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_MPI=ON -DGMX_GPU=ON
>
> But I encountered with error. The last lines are as follows:
>
>
> --
> -- gcc 4.4.7 detected, using -O3, will apply workaround for optimization
> bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
> -- Looking for include file unistd.h
> -- Looking for include file unistd.h - found
> -- Looking for include file pwd.h
> -- Looking for include file pwd.h - found
> -- Looking for include file dirent.h
> -- Looking for include file dirent.h - found
> -- Looking for include file time.h
> -- Looking for include file time.h - found
> -- Looking for include file sys/time.h
> -- Looking for include file sys/time.h - found
> -- Looking for include file io.h
> -- Looking for include file io.h - not found
> -- Looking for include file sched.h
> -- Looking for include file sched.h - found
> -- Looking for include file regex.h
> -- Looking for include file regex.h - found
> -- Looking for posix_memalign
> -- Looking for posix_memalign - found
> -- Looking for memalign
> -- Looking for memalign - not found
> -- Looking for _aligned_malloc
> -- Looking for _aligned_malloc - not found
> -- Looking for gettimeofday
> -- Looking for gettimeofday - found
> -- Looking for sysconf
> -- Looking for sysconf - found
> -- Looking for nice
> -- Looking for nice - found
> -- Looking for fsync
> -- Looking for fsync - found
> -- Looking for _fileno
> -- Looking for _fileno - not found
> -- Looking for fileno
> -- Looking for fileno - found
> -- Looking for _commit
> -- Looking for _commit - not found
> -- Looking for sigaction
> -- Looking for sigaction - found
> -- Looking for rsqrt
> -- Looking for rsqrt - not found
> -- Looking for rsqrtf
> -- Looking for rsqrtf - not found
> -- Looking for sqrtf
> -- Looking for sqrtf - found
> -- Looking for clock_gettime in rt
> -- Looking for clock_gettime in rt - found
> -- Looking for feenableexcept in m
> -- Looking for feenableexcept in m - found
> -- Checking for sched.h GNU affinity API
> -- Performing Test sched_affinity_compile
> -- Performing Test sched_affinity_compile - Success
> -- Check if the system is big endian
> -- Searching 16 bit integer
> -- Looking for sys/types.h
> -- Looking for sys/types.h - found
> -- Looking for stdint.h
> -- Looking for stdint.h - found
> -- Looking for stddef.h
> -- Looking for stddef.h - found
> -- Check size of unsigned short
> -- Check size of unsigned short - done
> -- Using unsigned short
> -- Check if the system is big endian - little endian
> -- MPI is not compatible with thread-MPI. Disabling thread-MPI.
> -- Found MPI_C:
>
> /opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
> -- Found MPI_CXX:
>
> /opt/openmpi/lib/libmpi_cxx.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
> -- Checking for MPI_IN_PLACE
> -- Performing Test MPI_IN_PLACE_COMPILE_OK
> -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
> -- Checking for MPI_IN_PLACE - yes
> -- Looking for zlibVersion in /usr/lib64/libz.so
> -- Looking for zlibVersion in /usr/lib64/libz.so - found
> -- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6")
> -- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.so
> -- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.so - found
> -- Looking for include file libxml/parser.h
> -- Looking for include file libxml/parser.h - found
> -- Looking for include file pthread.h
> -- Looking for include file pthread.h - found
> -- Atomic operations found
> -- Performing Test PTHREAD_SETAFFINITY
> -- Performing Test PTHREAD_SETAFFINITY - Success
> -- Could NOT find Boost
> Boost >= 1.44 not found. Using minimal internal version. This may cause
> trouble if you plan on compiling/linking other

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

2016-09-03 Thread Atila Petrosian

Dear gromacs users,

I am using Rocks cluster system with following info:

Rocks 6.2
CentOS 6.6
Cuda 7.5 and 8
gcc 4.4.7

I am installing gromacs-5.1.3. I used following command:

cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=ON
-DGMX_MPI=ON -DGMX_GPU=ON

But I encountered with error. The last lines are as follows:

--
-- gcc 4.4.7 detected, using -O3, will apply workaround for optimization
bug (disable with GMX_DISABLE_GCC44_BUG_WORKAROUND)
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file regex.h
-- Looking for include file regex.h - found
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Looking for _aligned_malloc
-- Looking for _aligned_malloc - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Looking for rsqrt
-- Looking for rsqrt - not found
-- Looking for rsqrtf
-- Looking for rsqrtf - not found
-- Looking for sqrtf
-- Looking for sqrtf - found
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Found MPI_C:
/opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
-- Found MPI_CXX:
/opt/openmpi/lib/libmpi_cxx.so;/opt/openmpi/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so;/usr/lib64/libm.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libdl.so
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Looking for zlibVersion in /usr/lib64/libz.so
-- Looking for zlibVersion in /usr/lib64/libz.so - found
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.7.6")
-- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.so
-- Looking for xmlTextWriterEndAttribute in /usr/lib64/libxml2.so - found
-- Looking for include file libxml/parser.h
-- Looking for include file libxml/parser.h - found
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Could NOT find Boost
Boost >= 1.44 not found. Using minimal internal version. This may cause
trouble if you plan on compiling/linking other software that uses Boost
against GROMACS.
-- Setting build user/date/host/cpu information
-- Setting build user & time - OK
-- Checking floating point format
-- Checking floating point format - IEEE754 (LE byte, LE word)
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for isfinite
-- Performing Test isfinite_compile_ok
-- Performing Test isfinite_compile_ok - Success
-- Checking for isfinite - yes
-- Checking for _isfinite
-- Performing Test _isfinite_compile_ok
-- Performing Test _isfinite_compile_ok -

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

Re: [gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

[gmx-users] CMake Error at cmake/gmxManageSimd.cmake:67 (message): Found a compiler flag for AVX2 support, but some other problem exists.

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