Are you using the ICC with EM64T extension?
I would like you to look at the nature of the program: GROMACS code is
unique as comparing to other computational software: its core code is
written in assembly code which simply can not be optimized further by
the compiler. What can be optimized is
In this version of GROMACS (3.3.1) there are no numbers displayed (I guess)... The way to choose your option is to just type in the terms... for eg. if you want to select Temperature just type out Temperature (or) Temp and hit ENTER. (It also works if you type out just a few letters in the word so
Hi all,I had similar problem with Fatal errors with Atomtype LC3 not found while setting up a POPC simulation. After a day of trying out different things I figured out the problem. And I would like to share my experience in the mailing list. Renaming of POP to POPC in the .gro files doesn't matter.
Hi All,i am using the g_energy command to look for the info in simulation, when i give the command this is what is get :-bash-2.05b$ g_energy_d :-) G R O M A C S (-: God Rules Over Mankind, Animals, Cosmos and Such
:-) VERS
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
Can you try to generate a backtrace for the mknb crash using gdb, in case this offers some insight?$ gdb mknbgdb> r -software_invsqrt...gdb> bt(backtrace output appears here)--TomOn May 31, 2006, at 11:33 AM, Jones de Andrade wrote:Hi David. First, thanks for your time. ;) Unfortunatelly, it seem
Hi, Jones
I can understand your sentiment after seeing these texts from Mars. I
shared the same when I was trying aggressive optimization (with Gentoo
Linux, FYI) and later with whatever software. But don't keep trying such
as it is not worthy the efforts you put (knowing the intrinsics of
sy
> 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 sure
> if they need to be
Jones de Andrade wrote:
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
Hi David.
And how could I do it? I mean, isn't mknb a significative piece of the code? What is it for? Would not that it yeld any problem?
And how to do it? Am I wrong, or should I first I run configure as it
is for gcc, save the mknb msakefile on it's directory, then configure
for icc, substitut
Jones de Andrade wrote:
Hi all.
Program received signal SIGSEGV, Segmentation fault.
0x2b15a88c in __find_specmb () from /lib64/tls/libc.so.6
(gdb) where
#0 0x2b15a88c in __find_specmb () from /lib64/tls/libc.so.6
#1 0x2b140e6f in vfprintf () from /lib64/tls/libc.so.6
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
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x2b15a88c in __find_specmb () from /lib64/tls/libc.so.6
> (gdb) where
> #0 0x2b15a88c in __find_specmb () from /lib64/tls/libc.so.6
> #1 0x2b140e6f in vfprintf () from /lib64/tls/libc.so.6
> #2 0x2b15e2
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
David van der Spoel wrote:
> The mknb_func.coul is of another type (a subset of int) there you can
> give its value to an integer, but not necessarily the other way around.
> I find it very unlikely that this would crash the program.
The enum and int variables should be the same size so the
ac
Jones de Andrade wrote:
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 copyin
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
Jones de Andrade wrote:
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.
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
> mknb_innerloop.c(362): warning #188: enumerated type mixed with
another type
> mknb_func.coul=coulsave;
> ^
I don't have the most recent source code on my machine,
but the way around this may be to use an explicit cast.
Assuming that
As have I. Very well, I have submitted a bugzilla (#84),
Arneh
Sukit Leekumjorn wrote:
Concerning the problem with g_order in Gromacs 3.3.1.
I did try fixing the problem as suggested, however, I could not get it
to work. In the mean time, I just use g_order from 3.3 version.
Sukit
Arneh B
Hi,
recently that I also went to in the research of this term. There were
once while some discussion on this list and many other papers.
(Look the whole thread of this post)
http://www.gromacs.org/pipermail/gmx-users/2003-January/003885.html
Tin-foil boundary is related to treatment of electr
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
Magdalena Siwko wrote:
Hi everybody,
can anyone tell me how to define tin-foil boundary conditions in mdp file?
There is nothing in the manual about it, actually.
eps_surface = 0
this is default IIRC
Thanks,
Magda
___
gmx-users mailing listgmx
Hi everybody,
can anyone tell me how to define tin-foil boundary conditions in mdp file?
There is nothing in the manual about it, actually.
Thanks,
Magda
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-u
Teje,
Yes i mean [pairs] section. I have read in manual this include 1-4
interaction, while using Oplsaa forcefield you need not to specify pairs as
they are automatically generated and if you are using RB dihedral this section
should be empty. I have few more question. The question may lo
Concerning the problem with g_order in Gromacs 3.3.1.
I did try fixing the problem as suggested, however, I could not get it
to work. In the mean time, I just use g_order from 3.3 version.
Sukit
Arneh Babakhani wrote:
Prof. Van Der Spoel,
Regarding your suggestion here: Where exactly are
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