hope I can make it work together with the IMPI. I don't want to
install openmpi as just a user also (did it a long time ago as root, not in
limited space).
Thanks again!
On Fri, Nov 8, 2013 at 9:21 AM, Mark Abraham wrote:
> On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade >wro
Really? An what about gcc+mpi? should I expect any improvement?
On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham wrote:
> You will do much better with gcc+openmp than icc-openmp!
>
> Mark
>
>
> On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade >wrote:
>
> > Did it a
Did it a few days ago. Not so much of a problem here.
But I compiled everything, including fftw, with it. The only error I got
was that I should turn off the separable compilation, and that the user
must be in the group video.
My settings are (yes, I know it should go better with openmp, but open
Hi.
I'm another one waiting for the OpenCL version here.
4.6 will support only CUDA.
>
> OpenCL GPU implementations have yet match CUDA; on CPU it would hardly
> match the performance of the hand-tuned SSE kernels, moreover, CPU &
> GPU algorithms are not the same.
>
If you allow me, the (second
Hi!
If I may ask, but what is the gromacs version that is planned on the roadmap
to begin to work with the newer version of openmm? Specially interested due
to ATI support
Regards
Jones
On Thu, Aug 18, 2011 at 10:01 PM, Szilárd Páll wrote:
> Hi,
>
> Gromacs 4.5.x works only with OpenMM 2.x. Yo
Hi all.
Sorry for waking up this subject again. But it rise a question for me:
Is gmx 4 or gmx 3.3 that has a bug so?
And, what is the bug concerned exactly? Buckingham interaction, 1-4
interactions, or buckingham 1-4 interactions?
Thanks a lot in advance,
Sincerally yours,
Jones
On Wed, May
Hi Justin.
On Mon, May 11, 2009 at 11:10 PM, Justin A. Lemkul wrote:
> All of the above can be fixed by changing the appropriate .mdp option.
Yes, I agree. I'll try that. Probably that's what will solve that problem.
If that's ok, I'll send to the site a "revised" version of the test set. :)
Shall I go straight to recompilation,
despite there is no reason for failure here?
Thanks a lot!
Jones
On Mon, May 11, 2009 at 10:42 PM, Jones de Andrade wrote:
> Hi Justin.
>
> Well, bothering again. Good and bad news.
>
> The good news: I found a strange "work-around&q
ipt, but since at least part of the tests worked, it means that it's
not the MPI that is, at least, missconfigured.
I will look deeper into the erros above, and tell you later.
Thanks a lot,
Jones
On Mon, May 11, 2009 at 9:41 PM, Jones de Andrade wrote:
> Hi Justin.
>
> Thanks a
emkul wrote:
>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> Jones de Andrade wrote:
>>
>>> Hi Justin
>>>
>>>This has been discussed several times on the list. The -np flag is
>>>no longer necessary with grompp. You don't
Hi Justin
This has been discussed several times on the list. The -np flag is no
> longer necessary with grompp. You don't get an mdrun.out because the .tpr
> file is likely never created, since grompp fails.
Yes, I know that and that is what I would have expected. But what I'm
running is the g
directories.
Version 3.3.3 on the other hand already failed in so many different places
that I'm really thinking IF I'll make it available in the new cluster. :P
This has to be any sort of pretty stupid mistake so. But I'm clueless this
time. :( Any ideas?
Thanks a lot in advance! :)
Jo
Hi everyone.
Well, lets go straight to the point: last time I've installed gromacs, it
was still 3.3.x and there was no testbed available yet. I've done some tests
of my own and everything gone fine.
I'm doing some new installations now, both gmx3.3.3 and gmx4.0.4. They weem
to work pretty well i
One point here is the fact that on specfp gromacs is NOT compiled with the
assembly parts. Those come from fortran. Performance hit, in different ways
from different architectures and compilers due to this. ;)
On Fri, Feb 13, 2009 at 10:04 AM, sobereva wrote:
>
> Hi,
>
> Gromacs is a test term o
Am I wrong, or are you considering some kind of MSCG (which is not into
gromacs at least in a standard, straight forward out of the box way)? That's
nice, would be really interesting to implement, would take long time and is
still a relativelly open-field with lot to be still explored.
I think we
Hi naimah.
Sorry for the late replay, but I was travelling. What kind of ionic liquids
are you interested in? If they are the dialkyl-immidazolium ones, I'm doing
simulations on these systems for quite some time now (please look at these
references: Journal of Physical Chemistry B, v. 112, p. 8966
Just addin my drop here:
Just did the same, both single and double precision, not parallel anyway.
What I get is the following:
*aurora down/gmxtest 41%* ./gmxtest.pl all
All 16 simple tests PASSED
FAILED. Check files in dec+water
1 out of 14 complex tests FAILED
All 63 kernel tests PASSED
All 4
Hi all.
I'm writing this message to ask a simple and direct question: the available
patch of gmx3 for slow networks, that includes the ordered-all-to-all
procedures, seems fo be indicated for version 3.1.
It's still "necessary" for slow networks using gmx3.3?
Thanks a lot in advance...
Sinceral
l test it a bit more, though.
Anyway, thanks a lot everybody for all help! :)
Sincerally yours,
Jones
On 10/11/07, Jones de Andrade <[EMAIL PROTECTED]> wrote:
>
> Hi all.
>
> Just informing, I tried a single molecule, and the topology with all
> dummies minimize (despite t
with many molecules or even single molecule MD, God?
Thanks a lot everybody in advance,
Sincerally yours,
Jones
On 10/11/07, Jones de Andrade <[EMAIL PROTECTED]> wrote:
>
> Hi Prof. David.
>
> Yes, it a self created topology. This one is based on another self created
> to
. Can you provide me some clue on
this?
I'll run a single molecule now.
Thanks a lot in advance,
Sincerally yours,
Jones
On 10/11/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
>
> Jones de Andrade wrote:
> > Hi Prof. David.
> >
> > What details do you mean?
Hi Prof. David.
What details do you mean? Actual topology files are attached. Anything else?
Thanks a lot in advance!
Sincerally yours,
Jones
On 10/11/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
>
> Jones de Andrade wrote:
> > Thanks Prof. David.
> >
> >
sion
problems, so or I missing something, of this assumption was completelly
wrong.
Thanks a lot in advance,
Sincerally yours
Jones
On 10/11/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
>
> Jones de Andrade wrote:
> > Hi all.
> >
> > Well, I'm having
Hi all.
Well, I'm having a bit of trouble here because the work has decided to go in
the direction of something I've never used before with gromacs: dummy atoms
(or now "virtual sites").
I've got at least three questions in order to use them:
1 - does the virtual sites need to be included in the
Hi Mark.
> I think those three can become yes in a really easy way: some kind of
> > "state machine" would easily do the trick and "count" them properly.
> Yes, but now you have to infer molecule changes from residue name
> changes, which is doable, but messy.
Forgot about this slice of the prob
Hi all.
First of all, I would really want want to apologize if I somehow
missunderstood any previous message from anyone, and made myself a bit
annoying because of this fact.
Second, I would like to say thanks again to eferybody for all help in these
matters.
On 10/1/07, Tsjerk Wassenaar <[EMAIL
nd sorry for taking so much of
your time,
Sincerally yours,
Jones
On 9/30/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
>
> Jones de Andrade wrote:
> > Hi Mark.
> >
> > Wait a second, you mean that editconf would allow me to have both
> > charges and masses on
Hi Mark.
Wait a second, you mean that editconf would allow me to have both charges
and masses on a .pdb file directly from command line (having other matters
asking for my presence absolutelly now, so please forgive me if this message
becomes somehow strange)
So, I would have atom names, number o
Again, tahnks a lot for all help in advance!
Sincerally yours,
Jones
On 9/30/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
>
> Mark Abraham wrote:
> > Jones de Andrade wrote:
> >> Hi Tsjerk.
> >>
> >> Thanks for the prompt answer.
> >>
&g
t; implementations for these... But maybe Bert knows better.
>
> Just one note... There's no shape in PBC. The lattice vectors are all
> there is, and these are stored in the .xtc file (as you already know).
>
> Cheers,
>
> Tsjerk
>
> On 9/30/07, Jones de Andrade <[
e Groot <[EMAIL PROTECTED]> wrote:
>
> On Sat, 29 Sep 2007, Jones de Andrade wrote:
>
> > Hi Bert.
> >
> > Thank you for the prompt answer.
> >
> > Just did as instructed, but got the following:
> >
> > CruNumMac src/own/B/9/xtc 286% ifort xtc
Hi Bert.
Thank you for the prompt answer.
Just did as instructed, but got the following:
CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90
-L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c
IPO link: can not find -lxrdf
ifort: error: problem during multi-file optimization compilation
Hi all.
I'm writing this beucase I'm having terrible problems in trying to deal with
gromacs trajectory files with my own programs, originally written on
fortran90.
The codes themselves are enoughly big to make it out of question to try to
"translate" them. What leads to some sort of mixed langua
Hi.
I'm trying to read some .xtc file trajectory files throw my fortran codes,
following the guidelines from
http://xray.bmc.uu.se/~spoel/md/online/xtc.html
Also later found this html file on the gromacs directory here. ;) Anyway,
I got stuck at some really strange point: I'm basically not find
to do this slice of the job by myself. ;)
Thanks a lot for your time, and please forgive me again for my "intrusion".
;)
Sincerally yours,
Jones
On 6/23/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
>
> Jones de Andrade wrote:
> > Hi Mark.
> >
> >
Hi Erik.
Still under NDA? Haven't it been lift last sunday?
Anyway: I don't know exactly the terms of the NDA, So if you can't answer me
the following question, please say "no, I can't answer". I'm in touch with
people having some compability issues with their Barcellonas and MBs, so
could you te
Hi.
Yes, but that is the "gcc solution". No prblem with those, except for giving
away the "challenge" to make it work with intel compilers.
Basically: I couldn't find a way much better. The way I trid in the time I
tried, included compilation of the loops and only the loops using gcc to
make the
Hi.
I would not agree with the fact that the approach isn't good.
The dialkylimidazolium cation class has a lot of interest on it, which
leaded to the development of force field for them rather than others.
It doesn't mean that there isn't force field for the [EtNH3]+ [NO3]- IL, but
means that t
Hi all.
Well, I have some kind of a "didatic" doubt: Ok, from what I can understand
up to now, PME uses lagrande interpolation for the genaration of the grid,
while SPME uses cardinal B-splines to do so.
Is it correct? And if, so, gromacs implements PME or SPME (the manual states
PME, but also st
Hi people.
Well, this thread is going to become an independet list for ILs.
We have developed a force field for a small set of cations and anions of
ILs, few year ago, based on AMBER. At the moment, we are (slowly) finalizing
publications on the extension of those for new sets of anions, all
comp
the original 5/10 steps frequency mdrun -rerun will update them every
> 5/10*10ps ...
>
> XAvier
>
> >>From: "Jones de Andrade" <[EMAIL PROTECTED]>
> >>Reply-To: Discussion list for GROMACS users
> >>To: "Discussion list for GROMAC
Hi both.
@ Mark: thanks mark. Have to admit that I haven't thought about the
exclusions possibility. Specially because I was looking for a simple way of
doing it without removing the dynamics related to these forces from the
simulation itself. So, changing the nexcl looked a bit easier to do.
@ B
tputs. :(
Any other thoughts?
Thanks a lot,
Jones
On 8/6/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
>
> Jones de Andrade wrote:
> > Hi all.
> >
> > Well, I'm trying to calculate an energy from my simulations, where
> > here stands only for the sum o
Hi all.
Well, I'm trying to calculate an energy from my simulations, where
here stands only for the sum of *intermolecular* vdw and coulombic terms,
and LJ(1-4) and coul(1-4). This means that I should find a way to exclude
any "1-5", "1-6", "1-7" and so on contributions for coulombic and vdw
ene
Hi all.
I think I'm having a really strange problem:
Well, I have some simulations being performed, and wanted to remove from the
bigger molecules any vdw or coulombic intramolecular interaction "longer"
than 1-4. So, from 1-5 included forward, I would like to remove from the
energetic calculatio
Hi all again.
Sorry for bothering all you with this dihedrals subject.
Well, I'm trying this in my .itp file:
**
[ dihedraltypes ]
; i j k l functphi (degree) cp
(kJ/mol.rad^2) mult(n)
CTCTNT
Hi all.
Well, I'm having a few problems in implementing an opls-like dihedral
potential, what mean, a serie of different periodic dihedral potentials.
After much problem with the RB potential conversion, Ifound on the net that
the 3.3.1 version of gromacs allows me to use sum of different periodi
in a bond CT-CT will be
defined by the potential described in the fourth line, correct?
If anyone could confirm or deny it for me that would be really helpfull.
Thanks a lot in advance for everything.
Jones
On 7/27/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
>
> Jones de Andr
Hi Mark.
Thanks a lot.
I'm already trying to find some clue in the manual. Anyway, what sort of
extra information could be usefull?
Thanks a lot again! ;)
Jones
On 7/26/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
>
> Jones de Andrade wrote:
> > Hi all.
> >
> &
Hi all.
I'm trying to implement a samll RB-potential for some molecules I'm working
with. I choosen to go following the files from opls-aa force field included
with gromacs. Unfortunatelly, I get this error:
"No default Proper Dih. types, using zeroes"
Which is quite strange, as the error latel
Hi all.
I was just wondering, and I even think this is a stupid question:
As well as there are the Lorentz-Berthelot combination rules (among others)
for the sigma and epsilon from Lennard-Jones parameters of different atom
types, how can the parameters from Buckingham potential of different ato
the help in
all this subject!
Sincerally yours,
Jones
On 6/23/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:
> Hi David.
>
> Well, as long as I can remember, I pushed the last gromacs sources at
> time (3.3.1) and just installed it. Anyway, mdrun tells
van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:
> Hi David.
>
> Well, as long as I can remember, I pushed the last gromacs sources at
> time (3.3.1) and just installed it. Anyway, mdrun tells me it is 3.3 and
> g_energy says it is 3.2.1 (in the run headers)
= 173529
gen_seed= 12041979
On 6/23/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:
> Hi all.
>
> First, I would like to apologize for the previous message. Maybe I've
> been too "harsh"? Sorry for that.
>
> Second, I would l
,
Jones
On 6/23/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:
> Hi David!
>
> Ha, so there is something extra? Thanks a lot :) I knew I was
> forgeting something.
>
> So how should I deal with it? I mean, what are the contibutions
kind of contribution can be lacking where?
Thanks a lot in advance,
Sincerally yours,
Jones
On 6/23/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:
> Hi David!
>
> Ha, so there is something extra? Thanks a lot :) I knew I was
> forgeting somet
something missing?
Thanks a lot!
Jones
On 6/23/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:
> Hi Mark.
>
> Haven't got exactly what you said. So let me rephrase myself:
>
> The CF4 molecule doesn't have dihedrals nor intramolecular L
Hi Mark.
Haven't got exactly what you said. So let me rephrase myself:
The CF4 molecule doesn't have dihedrals nor intramolecular LJ and coulombic
contributions.
What kind of contribution am I missing that makes potential energy minus
bond stretching minus angle bending *different* from Lj + co
Hi all.
Well, I have a question on the usage of g_energy.
I'm simulationg a really small test molecule, CF4. No problems with
parameter, even nmol flag was used.
My question(s) is a bit of usage or interpretation.
The intermolecular energy in the liquid should no be equal to the sum of the
LJ,
Hi!
I was just wondering: am I completelly wrong, or gromacs uses the BFGS
hessian approximation in order to do normal mode analysis, rather than the
"real and painfull to analitically second derive potentials" hessian?
I'm wondering also if this approximation is as good for NMA as it is for
min
' model):
http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp0706477.html
Their code is already working, but under the GROMOS software...
Ciao,
Patrick
Jones de Andrade a écrit :
> Hi David
>
> They have published a few paper on water and alcohols. The charm
crew
> have
Hi David
They have published a few paper on water and alcohols. The charm crew
have done a few more. Amber is actually split into two IIRC, with point
dipoles as well as shell models (that means either or).
I've found two papers for charmm polariability. But I'll only be able to try
to find i
<[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:
> Hi list.
>
> Well, a few days ago I've written a message concerning the future
> implementations that could be expected min gromacs 4 when it's released.
> Unfortunatelly, the thread hasn't gone any further.
lots
Hi list.
Well, a few days ago I've written a message concerning the future
implementations that could be expected min gromacs 4 when it's released.
Unfortunatelly, the thread hasn't gone any further.
So, I would like to know if there is somone in this list who ever tried to
modify gromacs progra
Hi Al..
Well, first of all sorry if this message becomes a bit out of the scope of
the list.
Since I've heard a lot of time ago somewhere in here that the gromacs
4.0was "in development", today I remembered that and decided to ask
google to
give this a try.
I basically found this 2 documents co
system,
correct?
Thanks a lot in advance!
Sincerally yours,
Jones
On 5/3/07, Erik Lindahl <[EMAIL PROTECTED]> wrote:
Hi,
On May 3, 2007, at 12:37 PM, Jones de Andrade wrote:
Hi Berk! Thanks for your so fast answer!
I'll try to look for a different tau_p. I would really feel 4 ps
On 5/3/07, Erik Lindahl <[EMAIL PROTECTED]> wrote:
Hi,
On May 3, 2007, at 12:37 PM, Jones de Andrade wrote:
Hi Berk! Thanks for your so fast answer!
I'll try to look for a different tau_p. I would really feel 4 ps a too
high value, even for water systems, but will look around befo
me to this question, and this is how this
ended:
**>* Hi,
*>*
*>* Just use the water value for any liquid system (5e-5 or so).
*>*
*>* As the manual explains, it only affects the coupling time, not the
*>* equilibrium pressure.
*>*
*>* Cheers,
*>*
*>* Erik
*>***
*>
Hi all.
Well, I'm having a great problem in some NpT simulations I'm running here,
which leaded me to some concerns. Let me try to explain the situation:
Ok, I know: everywhere, including this list, amber list and any
computational chemistry list informs that the compressibility of the liquid
do
file. Could you tell me which files should I look at, in
this case?
Thanks a lot in advance!
Jones
On 3/24/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:
> Hi David.
>
> I would say the .top files. .tpr are not of interest in this point,
> extra and unn
which ones should I look at?
Sorry for not making myself clear in the previous message.
Thanks a lot in advance,
Jones
On 3/24/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:
> Hi all!
>
> About the "same" subject... Does anybody ever tried to
Hi all!
About the "same" subject... Does anybody ever tried to read the topology
files from gromacs within fortran?
I would accept some C routines for this if necessary... :)
Thanks a lot,
Jones
On 3/24/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Hi Gurpreet,
Try to get your hands on t
Hi all.
first, thanks a lot! :)
Pedro: I've already expanded the box increadibly much (say, 200
angstrons in each direction), and the problem still remains. I mean,
expanded it from an original box with size to fit the experimental
density.
Low temperatures where already tested in the C9 but n
Hi everybody.
I would like to ask one question, basically about equilibration of
long and flexible alkyl chains.
I'm having terrible problems in equilibrating C8 and C9 chains. I've
already expanded a lot the box size, but I always fall into
segmentation faults. Also tried smaller time steps (my
d not have any problem, and reduce "independently" the 1 - 4 LJ
potentials by a factor of 0.5, and 1 - 4 coulombic interations by a
factor of 0.8333, correct?
Tnaks a lot in advance,
Sincerally yours,
Jones
On 2/13/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de And
Hi Erik.
Well, I don't even use the [pairtypes] section in my files. Only use
the [pairs] one, in the way explained before. This means, so, that it
should not have any problem, and reduce "independently" the LJ
potentials by a factor of 0.5, and coulombic interations by a factor
of 0.8333, correc
udgeLJ of 0.5, and the fudgeQQ of 0.8333 for 1-4
interactions, or should I make any kind of correction still?
Thanks a lot in advance for everything,
Sincerally yours,
Jones
On 2/13/07, Erik Lindahl <[EMAIL PROTECTED]> wrote:
Hi,
On Feb 13, 2007, at 6:52 AM, Jones de Andrade wrote:
&
Hi guys.
Well, I'm not "exactly" trying t reopen an old discussion. I'm trying to see
a different aspect from it, as the subject indicates.
Since the message reproduced below is the last of the "fudges" questions,
I'm worried about the fact of the fudgeLJ meaning nothing for the
simulation.
Fir
cores, etc.).
So, since I'm locked in a socket, I'm wandering what's better: the
highest clock possible, or less clock with two cores?
Thanks a lot...
Jones
On 8/1/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:
> Hi David.
>
> Well,
]> wrote:
Jones de Andrade wrote:
> Ok, I know this subject have been discussed in the past.
>
> But I started to wander if the basic conclusion (do not use in parallel,
> you should rather use on job for each core) is still up, and if it is,
> if there is any hope of change in a fo
Ok, I know this subject have been discussed in the past.
But I started to wander if the basic conclusion (do not use in
parallel, you should rather use on job for each core) is still up, and
if it is, if there is any hope of change in a foresight future, as well
on how much real loss is observed f
Hi all.
Well, I've been working in this for some time now, and it now seems to be a stable and clean and also "good looking" version.
Since I think I'm not the only one that, instead of making one long
simulation, prefers to make some or many simulations one after the
other, this might be of use.
Hi all!.I was trying to simulate a complex cation in MeCN solution and this called my attention: grompp gives me: "Generating 1-4 interactions: fudge = 0.5". It's not wrong, since I put this fudge for the VdW interactions, BUT I also placed a different fudge for the intramolecular coulombic interat
Hi all!.
I was trying to simulate a complex cation in MeCN solution and I got 2
strange warnings to me:
processing topology...
WARNING 1 [file "ff_emi.itp", line 7]:
Overriding atomtype CT
WARNING 2 [file "ff_emi.itp", line 11]:
Overriding atomtype H1
But I did found that strange because, as
Ok, I think I got it. Compiled. ;)
About a thousand tricks. I'll publish a tutorial later. But, basically:
1 - Change all invsrt calls to gmx_inv-sqrt (57 entries, 12 files);
2 - Edit the Makefile.in in the
nb_kernels directories, changing the line "LTCCASCOMPILE = $(LIBTOOL)
--mode=compile $(CCAS
Hi all.
Of course I want SSE enabled. There is no sense in benching it against
different compilers if in one you enable the speed and on the other,
and in the other you remove almost every optimization. That's why in
the last message I've sent the eror I'm getting in the compilation:
***
Hi all. :)
Last message today. It seems that I succeded in switching all "invsqrt"
functins to a new "gmx_invsqrt". Just 57 in the 12 files below:
***
include/vec.h
src/mdlib/csettle.c
src/mdlib/vsite.c
src/mdlib/clincs.c
src
Hi all.
On 6/1/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
> Trying withou the "-ipo" flag now. It still yelds the same weird warning
> (warning #147: declaration is incompatible with "double invsqrt(double)"> (declared at line 565 of "/usr/local/intel/include/math.h")rename all gromacs inv
Hi all!.
First, sorry for the delay in getting in touch again. Bureaucracy. :P
Second, thanks a lot for everybody for advising on this subject. It's helping me a lot to solve this! :)
Anyway, here is where I'm now:
Erik: I'm sure about the flags. Not using the ones for SSE3, despite my
Hi all.
First of all, thanks everybody for the help. ;)
Yang, I know, I know. I should keep to the GNU. But lets say that I get
addicted to the intel compiler on a cpmd winter school, when it
appeared in front of me as the only freely available for both amd and
intel cpus fortran90 compiler. Sinc
re
for icc, substitute it by the old Mkefile in the mknb directory and
then make? (Trying this now)
Thanks in advance for everything.
JonesOn 5/31/06, David van der Spoel <[EMAIL PROTECTED]> wrote:
Jones de Andrade wrote:> Hi all.> Program received signal SIGSEGV, Segmentation fault.&
Hi all!
Ok, got what should be done. But now I have a (big) question: this code
compiles properly with gcc. Ok, maybe that means difference of
tolerance between different compilers. But the code also compiles with
intel on intel machines, and seems to work properly on older amd
machines (not quite
Hi all.
Sorry for answering twice, but I tried a bit more with the debuggers
and, despite not finding how to fix what I'm doing wrong, I could get
some extra information:
Using "idb":
Intel(R) Debugger for Intel(R) EM64T -based Applications, Version 9.0-16, Build 20051121
(idb) load ./mkn
Hi David.
Well, here is what it yelds:
GNU gdb 6.3
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
Th
Hi David.
Thanks a lot. But almost there. first, coulsave is already n "int" type variable:
int vdwsave,coulsave,read_from_mem,write_to_mem; (line 294)
So, the change from:
mknb_func.coul=coulsave;
mknb_func.vdw=vdwsave;
To:
mknb_func.coul=(int)coulsave;
mknb_func.vdw=(int)vdwsave;
Was point
Hi David.
First, thanks for your time. ;)
Unfortunatelly, it seems that the simple flag it is not quite enough still... :(
If it was not a well known fact that intel compiler yelds you some
extra performance for gromacs, and if I would not want to try to make
QM/MM of gromacs+cpmd (and, in this
Hi all.
Ok, I admit that I've posted it before. But I still not finding the
error that makes the gromacs compilation with intel compilers not work
on my AMD64 machine here.
The error I get is still the following:
**
./mk
Hi Erik!
Normal simulations aren't using any linear algebra stuff at all. BLAS
& LAPACK are only useful when you do matrix stuff, for instance
normal mode analysis.
Ouch, obvious mistake. Sorry, apologize the error from someone programming too much
analysis tolls, rather than the simulation
Hi all!
Well, first of all, sorry if it's on the wrong gromacs list, but from
what I could see on the website I could not find a clear indication on
where to put benchmarks.
Anyway, some time ago I asked the list for help on making this
benchmarks, on which I want to compare different com
Hi!
Sorry if this message reaches the list twice, but Gmail doesn't let me
know if the list received it... seems that it stores somehow in the
same message if it comes back, so I just know when there are answers. :(
Anyway, thanks a lot in advance for any help in this subject!
Yours,
Jones
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