Re: Re: Re: [gmx-users] GPU-based workstation

[James Starlight]

Dear Dr. Pall!

Thank you for your suggestions!

Asumming that I have budget of 5000 $ and I want to build gpu-based desktop
on this money.

Previously I've used single 4 core i5 with GTX 670 and obtain average 10
ns\day performance for the 70k atoms systems (1.0 cutoffs, no virtual sites
, sd integrator).

Now I'd like to build system based on 2 hight-end GeForces (e.g like TITAN).
Should that system include 2 cpu's for good balancing? (e.g two 6 nodes
XEONS with faster clocks for instance could be better for simulations than
i7, couldnt it?)

What addition properties to the MB should I consider for such system ?

James

2013/5/28 lloyd riggs 

> Dear Dr. Pali,
>
> Thank you,
>
> Stephan Watkins
>
> *Gesendet:* Dienstag, 28. Mai 2013 um 19:50 Uhr
> *Von:* "Szilárd Páll" 
>
> *An:* "Discussion list for GROMACS users" 
> *Betreff:* Re: Re: [gmx-users] GPU-based workstation
> Dear all,
>
> As far as I understand, the OP is interested in hardware for *running*
> GROMACS 4.6 rather than developing code. or running LINPACK.
>
>
> To get best performance it is important to use a machine with hardware
> balanced for GROMACS' workloads. Too little GPU resources will result
> in CPU idling; too much GPU resources will lead to the runs being CPU
> or multi-GPU scaling bound and above a certain level GROMACS won't be
> able to make use of additional GPUs.
>
> Of course, the balance will depend both on hardware and simulation
> settings (mostly the LJ cut-off used).
>
> An additional factor to consider is typical system size. To reach near
> peak pair-force throughput on GPUs you typically need >20k-40k
> particles/GPU (depends on the architecture) and throughput drops below
> these values. Hence, in most cases it is preferred to use fewer and
> faster GPUs rather than more.
>
> Without knowing the budgdet and indented use of the machine it is hard
> to make suggestions, but I would say for a budget desktop box a
> quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a
> fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well.
> If you're considering dual-socket workstations, I suggest you go with
> the higher core-count and higher frequency Intel CPUs (6+ cores >2.2
> GHz), otherwise you may not see as much benefit as you would expect
> based on the insane price tag (especially if you compare to an i7
> 3939K or its IVB successor).
>
> Cheers,
> --
> Szilárd
>
>
> On Sat, May 25, 2013 at 1:02 PM, lloyd riggs  wrote:
> > More RAM the better, and the best I have seen is 4 GPU work station. I
> can
> > use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is
> > really 3-4 GPU, except the tyan mentioned (there designed as blades so
> an 8
> > or 10 slot board really holds 8 or 10 GPU's). There's cooling problems
> > though with GPU's, as on a board there packed, so extra cooling things
> may
> > help not blow a GPU, but I would look for good ones (ask around), as its
> a
> > video game market and they go for looks even though its in casing? The
> > external RAM (not onboard GPU RAM) helps if you do a larger sim, but I
> dont
> > know performance wise, the onboard GPU, the more RAM the marrier...so
> yes,
> > normal work stations you can get 4 GPU's for a 300 US$ board, but then
> the
> > price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad
> is
> > also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
> > software, not Gromacs, so would be nice to see performance...for a small
> 100
> > atom molecule and 500 solvent, using just the CPU I get it to run 5-10
> > minutes real for 1 ns sim, but tried simple large 800 amino, 25,000
> solvent
> > eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps
> > eq's
> >
> > Stephan
> >
> > Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
> > Von: "James Starlight" 
> > An: "Discussion list for GROMACS users" 
> > Betreff: Re: [gmx-users] GPU-based workstation
> > Dear Dr. Watkins!
> >
> > Thank you for the suggestions!
> >
> > In the local shops I've found only Core i7 with 6 cores (like Core
> > i7-39xx) and 4 cores. Should I obtain much better performance with 6
> cores
> > than with 4 cores in case of i7 cpu (assuming that I run simulation in
> > cpu+gpu mode )?
> >
> > Also you've mentioned about 4 PCeI MD. Does it means that modern
> > work-station could have 4 GPU's in one home-like desktop ? According to
> my
> > current task I suppose that 2 GPU's would be suitable for my simulations
> > (assuming that I use typical ASUS MB and 650 Watt power unit). Have
> > someone tried to use several GPU's on one workstation ? What attributes
> of
> > MB should be taken into account for best performance on such multi-gpu
> > station ?
> >
> > James
> >
> > 2013/5/25 lloyd riggs 
> >
> >> There's also these, but 1 chip runs 6K US, they can get performance up
> to
> >> 2.3 teraflops per chip though double percission...but have no clue about
> >> integration with GPU's...Intell also sells their chips

[gmx-users] Re: gmx-users Digest, Vol 109, Issue 153

[Ayesha Fatima]

 Compiling GROMACS w CUDA 5.0 problem
I did this a few days. i will share my how to do. i used gromacs 4.6.1.
assuming u have the nvidia gpu also

1.$ tar xfz gromacs-4.6.tgz

$ cd gromacs-4.6
$ mkdir build-cmake
$ cd build-cmake
$sudo apt-get install cmake
$ cmake ..
$cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
sudo apt-get install libfftw3-dev libfftw3-doc
$ CMAKE_PREFIX_PATH=/opt/fftw:/opt/cuda cmake ..
$cmake .. -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_mod
-DGMX_LIBS_SUFFIX=_mod
$ make -j 8$make install

$ source /usr/local/gromacs/bin/GMXRC

Running the file:

give the following input in the mdp file

cutoff-scheme = Verlet

regards

ayesha


On Mon, May 27, 2013 at 6:00 PM,  wrote:

> Send gmx-users mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
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>
> Today's Topics:
>
>1. Entropy (Yulian)
>2. Re: g_hbond (maggin)
>3. Re: mdrun outputs incorrect resnames (Reid Van Lehn)
>4. AMBER99 P450 heme topology (Parker de Waal)
>5. Compiling GROMACS w CUDA 5.0 problem (Jernej Zidar)
>
>
> --
>
> Message: 1
> Date: Sun, 26 May 2013 05:04:59 -0700 (PDT)
> From: Yulian 
> Subject: [gmx-users] Entropy
> To: gmx-users@gromacs.org
> Message-ID: <1369569899419-5008547.p...@n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Dear Gromacs users,
> There is a problem with entropy calculations with g_anaeig.
>
> I have 3 runs 100 ns each.
> Entropy for each run (Protein-H) is round 31000 J/mol K (100 ns)
> If I use trjcat to connect two trajectories it is  26000 J/mol K (200 ns)
> For three connect  trajectories it is round 19000 J/mol K
>
>
> I tried to do some checking:
> For example, I used 50 ns from one traj and 50 ns from the other in
> different combinations but it does not change the entropy value
> significantly. It seems that three runs are not so different.
>
> Also there is a problem with calculating of entropy on different machines.
> The result can be different for different machines (+/-  several hundreds
> of
> J/mol K for this system)
>
> I use gromacs-4.5.6.
> For all runs I  use "trjconv  -pbc nojump" before analysis.
> Thank you.
>
>  Yulian
>
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Entropy-tp5008547.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> --
>
> Message: 2
> Date: Sun, 26 May 2013 07:23:56 -0700 (PDT)
> From: maggin 
> Subject: [gmx-users] Re: g_hbond
> To: gmx-users@gromacs.org
> Message-ID: <1369578236451-5008548.p...@n6.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> Hi, Erik
>
> Thank you very much!Thank you!
>
> maggin
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/g-hbond-tp5008507p5008548.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
>
>
> --
>
> Message: 3
> Date: Sun, 26 May 2013 13:21:55 -0400
> From: Reid Van Lehn 
> Subject: Re: [gmx-users] mdrun outputs incorrect resnames
> To: Discussion list for GROMACS users 
> Message-ID:
> <
> cal_famm2ux_osqtsmmscd_fqgzd+c4cwrptgxen8udro2c4...@mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Great, thank you that did the trick. My fault for not realizing this
> earlier.
>
> Best,
> Reid
>
>
> On Sun, May 26, 2013 at 2:12 AM, Tsjerk Wassenaar 
> wrote:
>
> > No, the residue names are the those from the .top file. But that's not
> the
> > same as the moleculetypes. You have to change the residue names in the [
> > atoms ] section.
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Sun, May 26, 2013 at 12:57 AM, Mark Abraham  > >wrote:
> >
> > > AFAIK, the residue names in the mdrun output .gro file are those of the
> > > structure file you gave to grompp.
> > >
> > > Mark
> > >
> > >
> > > On Sun, May 26, 2013 at 12:31 AM, Reid Van Lehn 
> > > wrote:
> > >
> > > > Hello,
> > > >
> > > > I am simulating a lipid bilayer and wish to apply position restraints
> > to
> > > > only a subset of the lipids in the bilayer. Since position restraints
> > are
> > > > applied to all molecules of the same molecule type, I defined a new
> > > > molecule type (DOPR) which is identical to my lipid species (DOPC) by
> > > > copying the lipid itp file, renaming it and renaming the
> corresponding
> > > > molecule type. I then manually edited a starting .gro file to change
> a
> > > > subset of the DOPC molecules to DOPR, edited my topology,
> > > > renumbered/reordered, etc. I also r

[gmx-users] subspace overlap

[Miguel Ángel Mompeán García]

Dear all,

I am doing PCA on a 110ns run.
When calculating the subspace overlap from independent PCA performed in
different time windows, I expect the overlap to be 1 only when the time
interval is equal to 110ns, since both covariance matrices are identical.
However, I found that from the interval 0-70 forwards (I'm increasing each
window in 10ns) the overlap reaches that value. Is this expected? From the
rmsd, cosine content and visual inspection of the trajectory I expected
small changes from this point till the total time, but not the two matrices
being equal... Am I doing something wrong or this may happen?

Here is my data set of results:

Normalized Shape DT
0.6110.6380-10ns
0.6160.6500-20ns
0.6460.6710-30ns
0.6560.6780-40ns
0.6590.6830-50ns
0.8730.9190-60ns
1.0001.0000-70ns
1.0001.0000-80ns
1.0001.0000-90ns
1.0001.0000-100ns
1.0001.0000-110ns = Ttot
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Re: [gmx-users] arrange the atoms in sphere

[rajat desikan]

Use packmol.


On Wed, May 29, 2013 at 1:32 AM, dariush  wrote:

> Hello All,
>
> Does anybody have any script to arrange the molecules in the sphere?
> Actually, I need to set up a LDL (has hydrophobic core and monolayer of PC
> around).
>
> Thanks,
> Dariush
>
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/arrange-the-atoms-in-sphere-tp5008599.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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> www interface or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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[gmx-users] arrange the atoms in sphere

[dariush]

Hello All,

Does anybody have any script to arrange the molecules in the sphere?
Actually, I need to set up a LDL (has hydrophobic core and monolayer of PC
around).

Thanks,
Dariush



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/arrange-the-atoms-in-sphere-tp5008599.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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Aw: Re: Re: [gmx-users] GPU-based workstation

[lloyd riggs]

Dear Dr. Pali,

 

Thank you,

 

Stephan Watkins

 

Gesendet: Dienstag, 28. Mai 2013 um 19:50 Uhr
Von: "Szilárd Páll" 
An: "Discussion list for GROMACS users" 
Betreff: Re: Re: [gmx-users] GPU-based workstation

Dear all,

As far as I understand, the OP is interested in hardware for *running*
GROMACS 4.6 rather than developing code. or running LINPACK.


To get best performance it is important to use a machine with hardware
balanced for GROMACS' workloads. Too little GPU resources will result
in CPU idling; too much GPU resources will lead to the runs being CPU
or multi-GPU scaling bound and above a certain level GROMACS won't be
able to make use of additional GPUs.

Of course, the balance will depend both on hardware and simulation
settings (mostly the LJ cut-off used).

An additional factor to consider is typical system size. To reach near
peak pair-force throughput on GPUs you typically need >20k-40k
particles/GPU (depends on the architecture) and throughput drops below
these values. Hence, in most cases it is preferred to use fewer and
faster GPUs rather than more.

Without knowing the budgdet and indented use of the machine it is hard
to make suggestions, but I would say for a budget desktop box a
quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a
fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well.
If you're considering dual-socket workstations, I suggest you go with
the higher core-count and higher frequency Intel CPUs (6+ cores >2.2
GHz), otherwise you may not see as much benefit as you would expect
based on the insane price tag (especially if you compare to an i7
3939K or its IVB successor).

Cheers,
--
Szilárd


On Sat, May 25, 2013 at 1:02 PM, lloyd riggs  wrote:
> More RAM the better, and the best I have seen is 4 GPU work station. I can
> use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is
> really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8
> or 10 slot board really holds 8 or 10 GPU's). There's cooling problems
> though with GPU's, as on a board there packed, so extra cooling things may
> help not blow a GPU, but I would look for good ones (ask around), as its a
> video game market and they go for looks even though its in casing? The
> external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont
> know performance wise, the onboard GPU, the more RAM the marrier...so yes,
> normal work stations you can get 4 GPU's for a 300 US$ board, but then the
> price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad is
> also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
> software, not Gromacs, so would be nice to see performance...for a small 100
> atom molecule and 500 solvent, using just the CPU I get it to run 5-10
> minutes real for 1 ns sim, but tried simple large 800 amino, 25,000 solvent
> eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps
> eq's
>
> Stephan
>
> Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
> Von: "James Starlight" 
> An: "Discussion list for GROMACS users" 
> Betreff: Re: [gmx-users] GPU-based workstation
> Dear Dr. Watkins!
>
> Thank you for the suggestions!
>
> In the local shops I've found only Core i7 with 6 cores (like Core
> i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
> than with 4 cores in case of i7 cpu (assuming that I run simulation in
> cpu+gpu mode )?
>
> Also you've mentioned about 4 PCeI MD. Does it means that modern
> work-station could have 4 GPU's in one home-like desktop ? According to my
> current task I suppose that 2 GPU's would be suitable for my simulations
> (assuming that I use typical ASUS MB and 650 Watt power unit). Have
> someone tried to use several GPU's on one workstation ? What attributes of
> MB should be taken into account for best performance on such multi-gpu
> station ?
>
> James
>
> 2013/5/25 lloyd riggs 
>
>> There's also these, but 1 chip runs 6K US, they can get performance up to
>> 2.3 teraflops per chip though double percission...but have no clue about
>> integration with GPU's...Intell also sells their chips on PCIe cards...but
>> get only about 350 Gflops, and run 1K US$.
>>
>> http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor
>> http://www.xilinx.com/
>>
>> They can design them though to fit a PCIe slot and run about the same, but
>> still need the board, ram etc...
>>
>> Mostly just to dream about, they say you can order them with radiation
>> shielding as well...so...
>>
>> Stephan Watkins
>>
>> *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr
>> *Von:* "James Starlight" 
>> *An:* "Discussion list for GROMACS users" 
>> *Betreff:* [gmx-users] GPU-based workstation
>> Dear Gromacs Users!
>>
>>
>> I'd like to build new workstation for performing simulation on GPU with
>> Gromacs 4.6 native cuda support.
>> Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
>> and obtain good performance ( ~ 20 ns\day for typic

Re: [gmx-users] Re: GPU-based workstation

[Szilárd Páll]

On Tue, May 28, 2013 at 10:14 AM, James Starlight
 wrote:
> I've found GTX Titat with 6gb of RAM and 384 bit. The price of such card is
> equal to the price of the latest TESLA cards.

Nope!

Titan: $1000
Tesla K10: $2750
Tesla K20(c): $3000

TITAN is cheaper than any Tesla and the fastest of all NVIDIA GPUs (in
most cases).

>  Could it give me better performance in gromacs ?

The GROMACS GPU kernels are ~40% faster than on a GTX 680 and ~25%
faster than a K20, but when it comes to total performance, the
differences will obviously be smaller.

> Also assuming that 1 such card need 600 WATT power supply what supply I
> need for desktop with two such cards?

Nope. The peak power consumption of a TITAN is 250W and in
compute-only applications I doubt it draws more than max 70-80% of
that. With GROMACS as the GPU is only busy at most 70-80% of the time,
the effective consumption will scale roughly with those numbers. You
should use one of the online PSU calculators.

>
> 2013/5/28 Ehud Schreiber 
>
>> I have nothing to contribute regarding the CPUs, but note that last week
>> Nvidia introduced the GTX 780 GPU (a "Titan lite"), and this week it is
>> expected to introduce the GTX 770 one (probably an "overclocked 680").
>> Therefore, disregarding possible price issues, it seems that the GTX 680
>> may not be the best option.
>>
>>
>>
>> >Date: Mon, 27 May 2013 14:14:51 +0400
>>
>> >From: James Starlight > jmsstarli...@gmail.com>>
>>
>> >Subject: Re: Re: Re: [gmx-users] GPU-based workstation
>>
>> >To: Discussion list for GROMACS users > gmx-users@gromacs.org>>
>>
>> >Message-ID:
>>
>> > > vots3fvukbeky4k3pk27n2x...@mail.gmail.com> vots3fvukbeky4k3pk27n2x...@mail.gmail.com>>
>>
>> >Content-Type: text/plain; charset=ISO-8859-1
>>
>> >
>>
>> >On Nvidia benchmarks I've found suggestions of using of the two 6 cores
>> CPU for systems with the 2 GPU.
>>
>> >
>>
>> >Assuming that I'll be using two 680 GTX cards with 256 bits and 4gb ram
>> (not a profesional nvidia cards like TESLA) what CPU's >could give me the
>> best performance- 1 i7 of 8 cores or 2 Xeons e5 with 6 cores ? Does it
>> meaningful to use 2 separate CPU's with >several nodes each for the 2 GPU's
>> ?
>>
>> >
>>
>> >James
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>
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Re: Aw: Re: [gmx-users] GPU-based workstation

[Szilárd Páll]

On Sat, May 25, 2013 at 2:16 PM, Broadbent, Richard
 wrote:
> I've been running on my Universities GPU nodes these are one E5-xeon (6-cores 
> 12 threads)  and have 4 Nvidia 690gtx's. My system is 93 000 atoms of DMF 
> under NVE.  The performance has been a little disappointing

That sounds like a very imbalanced system for GROMACS, you have
essentially 8 GPUs with rather poor PCI-E performance (a board share a
single PCI-E bus) and only 12 CPU cores to "drive" the simulation.

~10ns/day. On my home system using a core i5-2500 and a nvidia 560ti I
get 5.4ns/day for the same system. On our HPC system using 32 nodes
each with 2 quad-core xeon processors I get 30-40ns/day.

That sounds somewhat low if these are all moderately fast CPUs and GPUs.

> I think that to achieve reasonable performance the system has to be balanced 
> between CPU's and GPU's probably getting 2 high end GPU's and a top end xeon 
> E5 or core i7 would be a good choice.

Indeed. Even two GPUs may be too much - unless the CPU in question is
a very high end i7 or E5.

Cheers,
--
Szilárd

>
>
> Richard
>
> From: lloyd riggs mailto:lloyd.ri...@gmx.ch>>
> Reply-To: Discussion users 
> mailto:gmx-users@gromacs.org>>
> Date: Saturday, 25 May 2013 12:02
> To: Discussion users mailto:gmx-users@gromacs.org>>
> Subject: Aw: Re: [gmx-users] GPU-based workstation
>
> More RAM the better, and the best I have seen is 4 GPU work station.  I can 
> use/have used 4.  The GPU takes 2 slots though, so a 7-8 PCIe board is really 
> 3-4 GPU, except the tyan mentioned (there designed as blades so an 8 or 10 
> slot board really holds 8 or 10 GPU's).  There's cooling problems though with 
> GPU's, as on a board there packed, so extra cooling things may help not blow 
> a GPU, but I would look for good ones (ask around), as its a video game 
> market and they go for looks even though its in casing?  The external RAM 
> (not onboard GPU RAM) helps if you do a larger sim, but I dont know 
> performance wise, the onboard GPU, the more RAM the marrier...so yes, normal 
> work stations you can get 4 GPU's for a 300 US$ board, but then the price 
> goes way up (3-4000 US$ for an 8-10 gpu board).  RAM ordered abroad is also 
> cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests software, 
> not Gromacs, so would be nice to see performance...for a small 100 atom 
> molecule and 500 solvent, using just the CPU I get it to run 5-10 minutes 
> real  for 1 ns sim, but tried simple large 800 amino, 25,000 solvent eq (NVT 
> or NPT) runs and they clock at around 1 hour real for say 50 ps eq's
>
> Stephan
>
> Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
> Von: "James Starlight" mailto:jmsstarli...@gmail.com>>
> An: "Discussion list for GROMACS users" 
> mailto:gmx-users@gromacs.org>>
> Betreff: Re: [gmx-users] GPU-based workstation
> Dear Dr. Watkins!
>
> Thank you for the suggestions!
>
> In the local shops I've found only Core i7 with 6 cores (like Core
> i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
> than with 4 cores in case of i7 cpu (assuming that I run simulation in
> cpu+gpu mode )?
>
> Also you've mentioned about 4 PCeI MD. Does it means that modern
> work-station could have 4 GPU's in one home-like desktop ? According to my
> current task I suppose that 2 GPU's would be suitable for my simulations
> (assuming that I use typical ASUS MB and 650 Watt power unit). Have
> someone tried to use several GPU's on one workstation ? What attributes of
> MB should be taken into account for best performance on such multi-gpu
> station ?
>
> James
>
> 2013/5/25 lloyd riggs mailto:lloyd.ri...@gmx.ch>>
>
>> There's also these, but 1 chip runs 6K US, they can get performance up to
>> 2.3 teraflops per chip though double percission...but have no clue about
>> integration with GPU's...Intell also sells their chips on PCIe cards...but
>> get only about 350 Gflops, and run 1K US$.
>>
>> http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor
>> http://www.xilinx.com/
>>
>> They can design them though to fit a PCIe slot and run about the same, but
>> still need the board, ram etc...
>>
>> Mostly just to dream about, they say you can order them with radiation
>> shielding as well...so...
>>
>> Stephan Watkins
>>
>> *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr
>> *Von:* "James Starlight" 
>> mailto:jmsstarli...@gmail.com>>
>> *An:* "Discussion list for GROMACS users" 
>> mailto:gmx-users@gromacs.org>>
>> *Betreff:* [gmx-users] GPU-based workstation
>> Dear Gromacs Users!
>>
>>
>> I'd like to build new workstation for performing simulation on GPU with
>> Gromacs 4.6 native cuda support.
>> Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
>> and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
>> with SD integrator)
>>
>>
>> Now I'd like to build multi-gpu wokstation.
>>
>> My question - How much GPU would give me best performance on the typical
>> home-like workstation. What algorit

[gmx-users] Re: choice of force field -reg

[David van der Spoel]

On 2013-05-28 18:09, Revthi Sanker wrote:

Dear Sir,
Thank you so much for your reply. To be specific, my system has only
four lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines.
But I was not able to get all atom paramters for these lipids from the
lipid book( only united atom parameters were available). So I had
resorted to using united atom for the whole system. But I am afraid if I
am missing out on some crucial protein-drug interactions because of this
united atom consideration.
Kindly guide me in this regard.


Sorry but you need to check literature and search the web. There are 
quite some resources out there. You might also look for Jochen Hub's web 
site.



Thank you so much once again.

Yours sincerely,
Revathi
M.S.Research Scholar
Indian Institute of Technology Madras
India




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
--
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Re: Re: [gmx-users] GPU-based workstation

[Szilárd Páll]

Dear all,

As far as I understand, the OP is interested in hardware for *running*
GROMACS 4.6 rather than developing code. or running LINPACK.


To get best performance it is important to use a machine with hardware
balanced for GROMACS' workloads. Too little GPU resources will result
in CPU idling; too much GPU resources will lead to the runs being CPU
or multi-GPU scaling bound and above a certain level GROMACS won't be
able to make use of additional GPUs.

Of course, the balance will depend both on hardware and simulation
settings (mostly the LJ cut-off used).

An additional factor to consider is typical system size. To reach near
peak pair-force throughput on GPUs you typically need >20k-40k
particles/GPU (depends on the architecture) and throughput drops below
these values. Hence, in most cases it is preferred to use fewer and
faster GPUs rather than more.

Without knowing the budgdet and indented use of the machine it is hard
to make suggestions, but I would say for a budget desktop box a
quad-core Intel Ivy Bridge or the top-end AMD Piledriver CPU with a
fast Kepler GTX card (e.g. GTX 680 or GTX 770/780) should work well.
If you're considering dual-socket workstations, I suggest you go with
the higher core-count and higher frequency Intel CPUs (6+ cores >2.2
GHz), otherwise you may not see as much benefit as you would expect
based on the insane price tag (especially if you compare to an i7
3939K or its IVB successor).

Cheers,
--
Szilárd


On Sat, May 25, 2013 at 1:02 PM, lloyd riggs  wrote:
> More RAM the better, and the best I have seen is 4 GPU work station.  I can
> use/have used 4.  The GPU takes 2 slots though, so a 7-8 PCIe board is
> really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8
> or 10 slot board really holds 8 or 10 GPU's).  There's cooling problems
> though with GPU's, as on a board there packed, so extra cooling things may
> help not blow a GPU, but I would look for good ones (ask around), as its a
> video game market and they go for looks even though its in casing?  The
> external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont
> know performance wise, the onboard GPU, the more RAM the marrier...so yes,
> normal work stations you can get 4 GPU's for a 300 US$ board, but then the
> price goes way up (3-4000 US$ for an 8-10 gpu board).  RAM ordered abroad is
> also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
> software, not Gromacs, so would be nice to see performance...for a small 100
> atom molecule and 500 solvent, using just the CPU I get it to run 5-10
> minutes real  for 1 ns sim, but tried simple large 800 amino, 25,000 solvent
> eq (NVT or NPT) runs and they clock at around 1 hour real for say 50 ps
> eq's
>
> Stephan
>
> Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
> Von: "James Starlight" 
> An: "Discussion list for GROMACS users" 
> Betreff: Re: [gmx-users] GPU-based workstation
> Dear Dr. Watkins!
>
> Thank you for the suggestions!
>
> In the local shops I've found only Core i7 with 6 cores (like Core
> i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
> than with 4 cores in case of i7 cpu (assuming that I run simulation in
> cpu+gpu mode )?
>
> Also you've mentioned about 4 PCeI MD. Does it means that modern
> work-station could have 4 GPU's in one home-like desktop ? According to my
> current task I suppose that 2 GPU's would be suitable for my simulations
> (assuming that I use typical ASUS MB and 650 Watt power unit). Have
> someone tried to use several GPU's on one workstation ? What attributes of
> MB should be taken into account for best performance on such multi-gpu
> station ?
>
> James
>
> 2013/5/25 lloyd riggs 
>
>> There's also these, but 1 chip runs 6K US, they can get performance up to
>> 2.3 teraflops per chip though double percission...but have no clue about
>> integration with GPU's...Intell also sells their chips on PCIe cards...but
>> get only about 350 Gflops, and run 1K US$.
>>
>> http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor
>> http://www.xilinx.com/
>>
>> They can design them though to fit a PCIe slot and run about the same, but
>> still need the board, ram etc...
>>
>> Mostly just to dream about, they say you can order them with radiation
>> shielding as well...so...
>>
>> Stephan Watkins
>>
>> *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr
>> *Von:* "James Starlight" 
>> *An:* "Discussion list for GROMACS users" 
>> *Betreff:* [gmx-users] GPU-based workstation
>> Dear Gromacs Users!
>>
>>
>> I'd like to build new workstation for performing simulation on GPU with
>> Gromacs 4.6 native cuda support.
>> Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
>> and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
>> with SD integrator)
>>
>>
>> Now I'd like to build multi-gpu wokstation.
>>
>> My question - How much GPU would give me best performance on the typical
>> home-like workstation. What a

Re: [gmx-users] choice of forcefield

[Mark Abraham]

You'll still need to do some reading. If your moieties have never been used
in all-atom simulations, you'll have a big task of parameterization, or
have to accept some approximation in your model. Even if they have been
used, you'll want to read up on how they were parameterized and whether
they've been shown to work well. Search the literature!

Mark


On Tue, May 28, 2013 at 6:12 PM, Revthi Sanker wrote:

>
>
> Dear Sir,
> Thank
>  you so much for your reply. To be specific, my system has only four
> lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I
> was not able to get all atom parameters for these lipids from the lipid
> book( only united atom parameters were available). So I had resorted to
> using united atom for the whole system. But I am afraid if I am missing
> out on some crucial protein-drug interactions because of this united
> atom consideration.
> Kindly guide me in this regard.
> Thank you so much once again.
>
> Yours sincerely,
> Revathi
> M.S.Research Scholar
> Indian Institute of Technology Madras
> India
>
>
> --- On Tue, 28/5/13, David van der Spoel  wrote:
>
> From: David van der Spoel 
> Subject: Re: [gmx-users] choice of forcefield
> To: gmx-users@gromacs.org
> Date: Tuesday, 28 May, 2013, 1:30 PM
>
> On 2013-05-28 14:39, massimo sandal wrote:
> > What other people do?
>
> Read literature. Gromacs allows you to choose many. If you need detailed
> results use an atomistic force field.
> >
> >
> > 2013/5/28 Dr. Vitaly Chaban 
> >
> >> In my mind, MARTINI is a decent option to build your particular topology
> >> upon.
> >>
> >> Dr. Vitaly Chaban
> >>
> >>
> >> On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker  >>> wrote:
> >>
> >>> Dear all,
> >>> I am a beginner to performing simulations and my system consists of
> >>> protein+ cholesteryl ester +phospholipid and drug. Papers involving
> >> lipids
> >>> are in general united atom, while those involving drug-protein systems
> >> are
> >>> all-atom mostly. Kindly suggest me which of these, all-atom or united
> >> atom
> >>> should I be using for my system.
> >>>
> >>> Thanks for your help in advance
> >>> Yours sincerely,
> >>> Revathi
> >>> M.S. Research Scholar
> >>> Indian Institute of Technology,Madras
> >>> India
> >>> --
> >>> gmx-users mailing listgmx-users@gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> * Please search the archive at
> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> * Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-requ...@gromacs.org.
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >> --
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> * Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:+46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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>
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Re: [gmx-users] About Compilation error in gromacs 4.6

[Mark Abraham]

That'll likely work, but whether Vidhya wants to use it depends whether he
cares about his simulation performance on this machine.

Mark


On Tue, May 28, 2013 at 4:05 PM, Mirco Wahab <
mirco.wa...@chemie.tu-freiberg.de> wrote:

> On 28.05.2013 13:39, vidhya sankar wrote:
>
>> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/**local/gromacs4.6 -DGMX_DOUBLE=ON
>> -DGMX_BINARY_SUFFIX=_d
>>
>
> please try
>
> cmake ..  -DGMX_CPU_ACCELERATION=SSE4.1 
> -DCMAKE_INSTALL_PREFIX=/usr/**local/gromacs4.6
> -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX=_d
>
> I remember to have encountered a problem with older gccs and AVX.
>
> M.
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
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Re: [gmx-users] Re: choice of force field -reg

[massimo sandal]

Chaban, why are you advising MARTINI? It is a coarse-grained force field,
one should be well aware of the limitations etc. before deciding to choose
it, it's not just "another force field".


2013/5/28 Dr. Vitaly Chaban 

> without knowing full details of your simulated system and the goals you
> pose, I cannot advise anything more definite than I did before.
>
> if I were you and my system were yours, I would start with MARTINI FF.
>
> I wish you a success in your endeavor.
>
> Dr. Vitaly Chaban
>
>
>
>
> On Tue, May 28, 2013 at 6:11 PM, Revthi Sanker  >wrote:
>
> >
> >
> > Dear Sir,
> > Thank you so much for your reply. To be specific, my system has only four
> > lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I
> was
> > not able to get all atom paramters for these lipids from the lipid book(
> > only united atom parameters were available). So I had resorted to using
> > united atom for the whole system. But I am afraid if I am missing out on
> > some crucial protein-drug interactions because of this united atom
> > consideration.
> > Kindly guide me in this regard.
> > Thank you so much once again.
> >
> > Yours sincerely,
> > Revathi
> > M.S.Research Scholar
> > Indian Institute of Technology Madras
> > India
> >
> >
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
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[gmx-users] Re: choice of force field -reg

[Dr. Vitaly Chaban]

without knowing full details of your simulated system and the goals you
pose, I cannot advise anything more definite than I did before.

if I were you and my system were yours, I would start with MARTINI FF.

I wish you a success in your endeavor.

Dr. Vitaly Chaban




On Tue, May 28, 2013 at 6:11 PM, Revthi Sanker wrote:

>
>
> Dear Sir,
> Thank you so much for your reply. To be specific, my system has only four
> lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I was
> not able to get all atom paramters for these lipids from the lipid book(
> only united atom parameters were available). So I had resorted to using
> united atom for the whole system. But I am afraid if I am missing out on
> some crucial protein-drug interactions because of this united atom
> consideration.
> Kindly guide me in this regard.
> Thank you so much once again.
>
> Yours sincerely,
> Revathi
> M.S.Research Scholar
> Indian Institute of Technology Madras
> India
>
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] choice of forcefield

[Revthi Sanker]

Dear Sir,
Thank
 you so much for your reply. To be specific, my system has only four 
lipid moities- 2 cholesteryl oleates and 2 phosphotidyl cholines. But I 
was not able to get all atom parameters for these lipids from the lipid 
book( only united atom parameters were available). So I had resorted to 
using united atom for the whole system. But I am afraid if I am missing 
out on some crucial protein-drug interactions because of this united 
atom consideration.
Kindly guide me in this regard.
Thank you so much once again.

Yours sincerely,
Revathi
M.S.Research Scholar
Indian Institute of Technology Madras
India


--- On Tue, 28/5/13, David van der Spoel  wrote:

From: David van der Spoel 
Subject: Re: [gmx-users] choice of forcefield
To: gmx-users@gromacs.org
Date: Tuesday, 28 May, 2013, 1:30 PM

On 2013-05-28 14:39, massimo sandal wrote:
> What other people do?

Read literature. Gromacs allows you to choose many. If you need detailed 
results use an atomistic force field.
>
>
> 2013/5/28 Dr. Vitaly Chaban 
>
>> In my mind, MARTINI is a decent option to build your particular topology
>> upon.
>>
>> Dr. Vitaly Chaban
>>
>>
>> On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker >> wrote:
>>
>>> Dear all,
>>> I am a beginner to performing simulations and my system consists of
>>> protein+ cholesteryl ester +phospholipid and drug. Papers involving
>> lipids
>>> are in general united atom, while those involving drug-protein systems
>> are
>>> all-atom mostly. Kindly suggest me which of these, all-atom or united
>> atom
>>> should I be using for my system.
>>>
>>> Thanks for your help in advance
>>> Yours sincerely,
>>> Revathi
>>> M.S. Research Scholar
>>> Indian Institute of Technology,Madras
>>> India
>>> --
>>> gmx-users mailing list    gmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>> --
>> gmx-users mailing list    gmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
sp...@xray.bmc.uu.se    http://folding.bmc.uu.se
-- 
gmx-users mailing list    gmx-users@gromacs.org
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Re: [gmx-users] About Warnings in Mdrun

[Mirco Wahab]

On 28.05.2013 17:11, vidhya sankar wrote:

As you Mailed Me I have compiled gromacs 4.6
I have installed using the command As posted in mail
But I have AMD 8 Core black Edition
When I run the mdrun I saw a warning
Note: file tpx version 73, software tpx version 83
Using 8 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, 
which is better)

What is the Meaning of the Above statement ?
How to raise the Performance


1) The meaning of the above statement:
Your machine is a newer AMD FX with a FMA (fused multiply/add)
execution unit. Your Gromacs is compiled for "older" architectures
having SSE (streaming SIMD extensions) version 4.1.
But you cannt use the AVX unit properly unless you upgrade your
gcc compiler to 4.7.x (maybe 4.6.x will work too). The older
gcc is not able to not generate the AVX instructions properly.

2) How to raise the performance:
The performance difference between AVX and SSE4.1 on an
AMF FX 8350 is marginal (I have a 8350 too) and can be
ignored for most real world scenarios. The speedup would
be 3%-5% with 4.6.1 for now, depending on the scenario
(chosen integrator, system size, electrostatics).

Much higher performance gains are to be expected by
properly configuring your system (cut off, integration
method etc.). This is an advanced topic in itself, please
read this
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
and this
http://www.gromacs.org/Documentation/Cut-off_schemes

Regards

M.

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Re: [gmx-users] About Warnings in Mdrun

[Justin Lemkul]

On 5/28/13 11:11 AM, vidhya sankar wrote:

Thank you Mirco Wahab  and Other Gromacs users
   As you 
Mailed Me I have compiled gromacs 4.6

I have installed using the command As posted in mail But I have AMD 8 Core 
black Edition

When I run the mdrun I saw a warning
Note: file tpx version 73, software tpx version 83
Using 8 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, 
which is better)

What is the Meaning of the Above statement ?


The tpx version indicates that you made the .tpr file with an older version than 
the one you are using to run the simulation.  That's not necessarily a problem, 
but .mdp settings and algorithms change between versions.


The second message is related to your problem before - your hardware can handle 
a better acceleration (AVX) but your compiler is too old to make use of it, so 
you had to downgrade to SSE4.1.  A new compiler will allow you to use the better 
acceleration.


-Justin

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[gmx-users] About Warnings in Mdrun

[vidhya sankar]

Thank you Mirco Wahab  and Other Gromacs users
  As you 
Mailed Me I have compiled gromacs 4.6 

I have installed using the command As posted in mail But I have AMD 8 Core 
black Edition 

When I run the mdrun I saw a warning
Note: file tpx version 73, software tpx version 83
Using 8 MPI threads
Compiled acceleration: SSE4.1 (Gromacs could use AVX_128_FMA on this machine, 
which is better)

What is the Meaning of the Above statement ?
How to raise the Performance
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Re: [gmx-users] About Compilation error in gromacs 4.6

[Mirco Wahab]

On 28.05.2013 13:39, vidhya sankar wrote:

cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON 
-DGMX_BINARY_SUFFIX=_d


please try

cmake ..  -DGMX_CPU_ACCELERATION=SSE4.1 
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON 
-DGMX_BINARY_SUFFIX=_d


I remember to have encountered a problem with older gccs and AVX.

M.

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Re: [gmx-users] Re: QM/MM simulations

[Justin Lemkul]

On 5/28/13 6:03 AM, DavidPO wrote:

Thank you.

Can you tell me whether there was such a problem in earlier versions?
If not, I could use for example version 4.5.7. Because I think it isn't very
important at first stage of experiment.



I have no idea.  Try 4.5.7 and see.  If it does work in 4.5.7, please let us 
know.

-Justin

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Re: [gmx-users] Lennard Jones parameters

[Justin Lemkul]

On 5/28/13 1:01 AM, Ishwor wrote:

Dear all
I want to study the simulation of Carbonmonoxide in water. I have seen the
Lennard Jones parameters, force constant and partial charges of water in the
file spce.itp inherent in gromacs but couldnt get the parameters for CO .I
will be pleased if anyone provide me the LJ parameters (epsilon and sigma)
,partial charge of Carbon Monoxide.Due to some technical diffculties I have
got no access for the published papers.  Thanks



Having access to the literature will be essential for continuing your work.  In 
any case, doing such a simulation is not as simple as "give me the parameters 
for molecule X."  You need to choose a parent force field that will represent 
your system and obtain or derive compatible parameters.  Parameterization is no 
easy task (although a diatomic molecule should be fairly straightforward), and 
you need to be very familiar with how the chosen force field works and is 
derived, information that will require thorough examination of the literature.


-Justin

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Re: [gmx-users] About Compilation error in gromacs 4.6

[Szilárd Páll]

10.04 comes with gcc 4.3 and 4.4 which should both work (we even test
them with Jenkins).

Still, you should really get a newer gcc, especially if you have an
8-core AMD CPU (=> either Bulldozer or Piledriver) both of which are
fully supported only by gcc 4.7 and later. Additionally, AFAIK the
2.6.32 kernel is not really optimal for these CPUs.

--
Szilárd


On Tue, May 28, 2013 at 3:01 PM, Mark Abraham  wrote:
> The actual error message is higher up, but my guess would be your compiler
> in 10.04 is too old to be useful. Per the installation instructions, you
> will want the latest version of gcc you can get, and ones that came with
> 10.04 will very likely be wrong or slower than the latest ones.
>
> Mark
>
>
> On Tue, May 28, 2013 at 1:39 PM, vidhya sankar wrote:
>
>> Dear Justin Thank you for your Previous reply,
>> I have
>> Downloaded gromacs 4.6
>>
>> I have configured well using the following command
>> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON
>> -DGMX_BINARY_SUFFIX=_d
>>
>> and when i Compile using make command
>> I have got following error
>> make[2]: ***
>> [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_avx_128_fma_double.c.o]
>> Error 1
>> make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
>> make: *** [all] Error 2
>>
>> How to solve the error
>> What  Dependencies should I install to solve This Error
>>
>> I Have installed gCC ,g++ compiler and fftw3.3 in My Ubuntu 10.04 OS
>>
>>   I have AMD 8 core processor
>> Thanks In Advance
>>
>> --
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>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] choice of forcefield

[David van der Spoel]

On 2013-05-28 14:39, massimo sandal wrote:

What other people do?


Read literature. Gromacs allows you to choose many. If you need detailed 
results use an atomistic force field.



2013/5/28 Dr. Vitaly Chaban 


In my mind, MARTINI is a decent option to build your particular topology
upon.

Dr. Vitaly Chaban


On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker 
wrote:



Dear all,
I am a beginner to performing simulations and my system consists of
protein+ cholesteryl ester +phospholipid and drug. Papers involving

lipids

are in general united atom, while those involving drug-protein systems

are

all-atom mostly. Kindly suggest me which of these, all-atom or united

atom

should I be using for my system.

Thanks for your help in advance
Yours sincerely,
Revathi
M.S. Research Scholar
Indian Institute of Technology,Madras
India
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Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] About Compilation error in gromacs 4.6

[Mark Abraham]

The actual error message is higher up, but my guess would be your compiler
in 10.04 is too old to be useful. Per the installation instructions, you
will want the latest version of gcc you can get, and ones that came with
10.04 will very likely be wrong or slower than the latest ones.

Mark


On Tue, May 28, 2013 at 1:39 PM, vidhya sankar wrote:

> Dear Justin Thank you for your Previous reply,
> I have
> Downloaded gromacs 4.6
>
> I have configured well using the following command
> cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON
> -DGMX_BINARY_SUFFIX=_d
>
> and when i Compile using make command
> I have got following error
> make[2]: ***
> [src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_avx_128_fma_double.c.o]
> Error 1
> make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
> make: *** [all] Error 2
>
> How to solve the error
> What  Dependencies should I install to solve This Error
>
> I Have installed gCC ,g++ compiler and fftw3.3 in My Ubuntu 10.04 OS
>
>   I have AMD 8 core processor
> Thanks In Advance
>
> --
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Re: [gmx-users] choice of forcefield

[massimo sandal]

What other people do?


2013/5/28 Dr. Vitaly Chaban 

> In my mind, MARTINI is a decent option to build your particular topology
> upon.
>
> Dr. Vitaly Chaban
>
>
> On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker  >wrote:
>
> > Dear all,
> > I am a beginner to performing simulations and my system consists of
> > protein+ cholesteryl ester +phospholipid and drug. Papers involving
> lipids
> > are in general united atom, while those involving drug-protein systems
> are
> > all-atom mostly. Kindly suggest me which of these, all-atom or united
> atom
> > should I be using for my system.
> >
> > Thanks for your help in advance
> > Yours sincerely,
> > Revathi
> > M.S. Research Scholar
> > Indian Institute of Technology,Madras
> > India
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] About Compilation error in gromacs 4.6

[vidhya sankar]

Dear Justin Thank you for your Previous reply,
    I have 
Downloaded gromacs 4.6 

I have configured well using the following command
cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs4.6 -DGMX_DOUBLE=ON 
-DGMX_BINARY_SUFFIX=_d

and when i Compile using make command 
I have got following error
make[2]: *** 
[src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_avx_128_fma_double.c.o]
 Error 1
make[1]: *** [src/gmxlib/CMakeFiles/gmx.dir/all] Error 2
make: *** [all] Error 2

How to solve the error 
What  Dependencies should I install to solve This Error

I Have installed gCC ,g++ compiler and fftw3.3 in My Ubuntu 10.04 OS

  I have AMD 8 core processor 
Thanks In Advance

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Re: [gmx-users] choice of forcefield

[Dr. Vitaly Chaban]

In my mind, MARTINI is a decent option to build your particular topology
upon.

Dr. Vitaly Chaban


On Tue, May 28, 2013 at 8:22 AM, Revthi Sanker wrote:

> Dear all,
> I am a beginner to performing simulations and my system consists of
> protein+ cholesteryl ester +phospholipid and drug. Papers involving lipids
> are in general united atom, while those involving drug-protein systems are
> all-atom mostly. Kindly suggest me which of these, all-atom or united atom
> should I be using for my system.
>
> Thanks for your help in advance
> Yours sincerely,
> Revathi
> M.S. Research Scholar
> Indian Institute of Technology,Madras
> India
> --
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Re: [gmx-users] Gromacs for Non biological systems

[Dr. Vitaly Chaban]

Look for my papers. At least, two dozens of them are about non-biophysical
stuff.

Gromacs can. The question is whether you can provide an adequate
Hamiltonian to describe your systems involving Al-surface.

Dr. Vitaly Chaban




On Mon, May 27, 2013 at 10:59 PM, Jeya vimalan wrote:

> Dear Collegues,
> I was pointed to Gromacs to make it work
> on the non biological systems.
> My aim is to understand the interaction
> of Hf precursors on Gamma Alumina surface.
> But, i do not know yet if gromacs can efficiently handle this.
> Can someone help me fiding some papers where GROMACS have been used for the
> non biological system.
> jeya
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[gmx-users] Re: QM/MM simulations

[DavidPO]

Thank you. 

Can you tell me whether there was such a problem in earlier versions?
If not, I could use for example version 4.5.7. Because I think it isn't very
important at first stage of experiment.

Best regards,
David



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Re: [gmx-users] Re: GPU-based workstation

[James Starlight]

I've found GTX Titat with 6gb of RAM and 384 bit. The price of such card is
equal to the price of the latest TESLA cards. Could it give me better
performance in gromacs ?

Also assuming that 1 such card need 600 WATT power supply what supply I
need for desktop with two such cards?

2013/5/28 Ehud Schreiber 

> I have nothing to contribute regarding the CPUs, but note that last week
> Nvidia introduced the GTX 780 GPU (a "Titan lite"), and this week it is
> expected to introduce the GTX 770 one (probably an "overclocked 680").
> Therefore, disregarding possible price issues, it seems that the GTX 680
> may not be the best option.
>
>
>
> >Date: Mon, 27 May 2013 14:14:51 +0400
>
> >From: James Starlight  jmsstarli...@gmail.com>>
>
> >Subject: Re: Re: Re: [gmx-users] GPU-based workstation
>
> >To: Discussion list for GROMACS users  gmx-users@gromacs.org>>
>
> >Message-ID:
>
> >  vots3fvukbeky4k3pk27n2x...@mail.gmail.com vots3fvukbeky4k3pk27n2x...@mail.gmail.com>>
>
> >Content-Type: text/plain; charset=ISO-8859-1
>
> >
>
> >On Nvidia benchmarks I've found suggestions of using of the two 6 cores
> CPU for systems with the 2 GPU.
>
> >
>
> >Assuming that I'll be using two 680 GTX cards with 256 bits and 4gb ram
> (not a profesional nvidia cards like TESLA) what CPU's >could give me the
> best performance- 1 i7 of 8 cores or 2 Xeons e5 with 6 cores ? Does it
> meaningful to use 2 separate CPU's with >several nodes each for the 2 GPU's
> ?
>
> >
>
> >James
>
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