[Molvis-list] hardware upgrades to increase rasmol performance on
very large systems.
Keith McLaughlin
kmclau at gmail.com
Thu May 24 17:52:23 EDT 2007
Hi all.
I am currently trying to find a way to read binary files into rasmol, rather
than having to convert to xyz first. Here is the code that I use to convert
from bin to xyz, which I'd like to integrate into rasmol. Any tips or ideas
wqhere I should start?
char symbol[2];
float pos[3];
REALYL EatomRB;
} singleatom;
main (int argc, char * argv[])
{
FILE * fp; int flen,np,npread; REALYL Axyz[3]; REALYL curtime;
singleatom * atoms, * atomsformated; unsigned char buffer[1024]; int i;
if (argc < 2) {
fprintf(stderr, "Usage: bin2xyz <file.bin>\n");
return;
}
fp = fopen (argv[1],"rb");
if (fp == NULL) {
fprintf(stderr, "ERROR: <%s> not found!\n",argv[1]);
return;
}
fseek(fp,0,SEEK_SET);
fread(&flen,sizeof(flen),1,fp);
fread(&np,sizeof(np),1,fp);
fread(Axyz,sizeof(REALYL),3,fp);
fread(&curtime,sizeof(REALYL),1,fp);
atoms=malloc(sizeof(singleatom)*(np+1));
atomsformated=atoms+np;
if (atoms == NULL) {
fprintf(stderr, "ERROR: Out of memory!\n");
return;
}
#ifdef DEBUG
fread(buffer,12*4,1,fp);
for (i=0;i<12*4;i++) fprintf(stdout,"%02X ",buffer[i]);
fprintf(stdout,"\n");
return;
#endif
npread=fread(atoms,22,np,fp);
if (npread < np) {
fprintf(stderr, "WARNING: data record truncated! Expecting %d , found %d
.\n",np,npread);
}
fprintf(stdout, " %d\n %lf %lf %lf %lf (fs)\n", npread,
Axyz[0],Axyz[1],Axyz[2],curtime);
for (i=0;i<npread;i++) {
memmove (atomsformated,(char *) atoms +i*22,2);
memmove (&(atomsformated->pos[0]),(char *) atoms +i*22+2,20);
fprintf(stdout, "%c%c %20.4lf %20.4lf %20.4lf %20.10lf\n",
atomsformated->symbol[0],atomsformated->symbol[1],
atomsformated->pos[0],atomsformated->pos[1],atomsformated->pos[2],
atomsformated->EatomRB);
}
free(atoms);
fclose(fp);
}
On 4/15/07, Keith McLaughlin <kmclaugh at physics.cas.usf.edu> wrote:
>
> Disregard that last issue I had. I found the 2.7.1 src and was able to
> compile it without any problems. Thanks a bunch. You've been a huge help.
>
> Keith McLaughlin
>
> On 4/15/07, Keith McLaughlin <kmclaugh at physics.cas.usf.edu> wrote:
> >
> > Herbert,
> >
> > The workstation I use is 1240x1028, but we are also experimenting with a
> > visual cluster with 4096x2304.
> >
> > I tried to compile after changing graphics.h, and a lot of this cc:
> > unrecognized option `-no-cpp-precomp'. When I try to load an atom, I crash
> > with the error "too many new atom types." Here is my entire output:
> >
> > [16:41:22 | scandium]<~/Desktop/RasMol_2.7.2.1.1/src>$ make
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o rasmol.o rasmol.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o molecule.o molecule.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o abstree.o abstree.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o cmndline.o cmndline.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o command.o command.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o transfor.o transfor.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o render.o render.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o repres.o repres.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o x11win.o x11win.c
> > cc: unrecognized option `-no-cpp-precomp'
> > x11win.c: In function `HandleIPCCommand':
> > x11win.c:2228: warning: dereferencing type-punned pointer will break
> > strict-aliasing rules
> > x11win.c :2265: warning: dereferencing type-punned pointer will break
> > strict-aliasing rules
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o pixutils.o pixutils.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o outfile.o outfile.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o script.o script.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o infile.o infile.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o tokens.o tokens.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o cif_fract.o cif_fract.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o cif.o cif.c
> > cc: unrecognized option `-no-cpp-precomp'
> > cif.c: In function `cif_free_node':
> > cif.c:494: warning: dereferencing type-punned pointer will break
> > strict-aliasing rules
> > cif.c: In function `cif_copy_string':
> > cif.c:1331: warning: dereferencing type-punned pointer will break
> > strict-aliasing rules
> > cif.c:1340: warning: dereferencing type-punned pointer will break
> > strict-aliasing rules
> > cif.c: In function `cif_free_string':
> > cif.c:1357: warning: dereferencing type-punned pointer will break
> > strict-aliasing rules
> > cif.c: In function `cif_free_handle':
> > cif.c:1385: warning: dereferencing type-punned pointer will break
> > strict-aliasing rules
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o cif_ctonum.o cif_ctonum.c
> > cc: unrecognized option `-no-cpp-precomp'
> > cif_ctonum.c:191:1: warning: "_USE_RASMOL_H_" redefined
> > <command line>:7:1: warning: this is the location of the previous
> > definition
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o cif_stx.o cif_stx.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o multiple.o multiple.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o vector.o vector.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o wbrotate.o wbrotate.c
> > cc: unrecognized option `-no-cpp-precomp'
> > /usr/bin/cc -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -I/usr/X11R6/include -D__powerpc__ -D__DARWIN__ -DNO_ALLOCA
> > -DX_LOCALE -DRASMOLDIR=\"/usr/X11R6/lib/rasmol/\" -DTHIRTYTWOBIT
> > -D_USE_RASMOL_H_ -c -o langsel.o langsel.c
> > cc: unrecognized option `-no-cpp-precomp'
> > rm -f rasmol
> > /usr/bin/cc -o rasmol -g -O2 -Wall -Wpointer-arith -no-cpp-precomp
> > -L/usr/X11R6/lib rasmol.o molecule.o abstree.o cmndline.o command.o
> > transfor.o render.o repres.o x11win.o pixutils.o outfile.o
> > script.o infile.o tokens.o cif_fract.o cif.o cif_ctonum.o
> > cif_stx.o multiple.o vector.o wbrotate.o langsel.o -lm -lXi -lXext
> > -lX11
> > cc: unrecognized option `-no-cpp-precomp'
> > rm -f rasmol._man
> > cd `dirname rasmol` && \
> > ln -s `basename rasmol.man` `basename rasmol._man`
> >
> > Additionally, I'd prefer source for 2.7.1, but not sure where to find
> > that. The issue I had with 2.7.2 with the colors is mentioned on the
> > README page:
> >
> > > This release is not fully debugged and has some serious problems. This
> > > release is intended for testing and experimentation and not for production
> > > use. Comments and suggestions would be appreciated. We are aware fo the
> > > following deficiencies:
> > >
> > > - RasMol may have difficulty in allocating colors for molecules
> > > after the first. The fix for this interacts with some other pending changes,
> > > and should be ready for the next release.
> > >
> > >
> >
> > Thanks a lot for your help Herbert!
> >
> > Sincerely,
> > Keith McLaughlin
> >
> >
> >
> >
> > On 4/14/07, Herbert J. Bernstein <yaya at bernstein-plus-sons.com> wrote:
> > >
> > > You should be able to automate the set write on command by using an
> > > external script or by redirecting stdin. The redirected file must end
> > > with the execution of your script and the exit command.
> > >
> > > I'll add a command to set the screen size from the command line,
> > > but until that is ready, it is easy to change the startup default
> > > size in a rebuild by changing the values DefaultWide and DefaultHigh
> > > in graphics.h. If you send me your screen dimensions, I'll make you
> > > such a binary.
> > >
> > > -- Herbert
> > >
> > >
> > > At 7:01 PM -0400 4/14/07, Keith McLaughlin wrote:
> > > >Thanks for your feedback. I will try to monitor the memory
> > > consumption and
> > > >such and I'll update.
> > > >
> > > >Closing rasmol between runs is not an option unless there is a way to
> > > make
> > > >rasmol automatically open fullscreen. Additionally, I believe the
> > > command
> > > >"set write on" needs to be entered manually. I'm not sure that it is
> > > >possible to automate this.
> > > >
> > > >On 4/13/07, Dr. Christoph Gille <christoph.gille at charite.de > wrote:
> > > >>
> > > >>
> > > >>I do not think that increasing
> > > >>RAM would solve the problem.
> > > >>
> > > >>If the RAM would be a problem the entire computer would be
> > > >>frozen.
> > > >>
> > > >>Since the computer is still responsive it has sufficient memory.
> > > >>
> > > >>Nevertheless,
> > > >>can you monitor memory consumption i.e.
> > > >>calling ps aux | fgrep rasmol ... after each image
> > > >>or using top or gps or whatever monitor.
> > > >>
> > > >>As a solution, can you close the rasmol instance in your script
> > > >>and start a new one
> > > >>after 400 files ?
> > > >>
> > > >>If the number of written files is about the
> > > >>same each time
> > > >>independently of the size of the protein
> > > >>it could also be that file pointers are not closed.
> > > >>
> > > >>You could have a look at the
> > > >>source code and check whether
> > > >>the file pointers are closed.
> > > >>
> > > >>
> > > >>
> > > >>> Hello all;
> > > >>>
> > > >>> My research involves 4 million atom MD simulations and we've
> > > decided to
> > > >>use
> > > >>> rasmol for visualization. From my experiences, I have two
> > > questions and
> > > >>am
> > > >>> hoping that someone here may be able to help.
> > > >>>
> > > >>> 1. Currently I'm using version 2.7.1 because it doesn't have the
> > > >>coloring
> > > >>> problems when loading images one after another. Unfortunately,
> > > after
> > > >>about
> > > >>> 500 images rasmol gives an error and is unable to load any new
> > > images
> > > >>saying
> > > >>> that the file is not found, or something to that effect. Does
> > > anyone
> > > >>have
> > > >>> experience with handling this?
> > > >>>
> > > >>> 2. We are planning on some upgrades, and are kind of curious as
> > > to which
> > > >>> components will help the most with increasing the speed in which
> > > these
> > > >>files
> > > >>> are loaded: memory or video memory, or perhaps processor. We
> > > mostly
> > > >>suspect
> > > >>> that adding more memory would be the best choice, but I'd like to
> > > hear
> > > >>other
> > > >>> opinions.
> > > >>>
> > > >>> Thanks!
> > > >>> --
> > > >>> Keith McLaughlin
> > > >>> University of South Florida
> > > >>> Physics Dept. PHY225
> > > >>> 4202 E. Fowler Ave
> > > >>> Tampa, FL 33620
> > > >>>
> > > >>> --
> > > >>> Keith McLaughlin
> > > >>> University of South Florida
> > > >>> Physics Dept. PHY225
> > > >>> 4202 E. Fowler Ave
> > > >>> Tampa, FL 33620
> > > >>> _______________________________________________
> > > >>> Molvis-list mailing list
> > > >>> Molvis-list at bioinformatics.org
> > > >>> https://bioinformatics.org/mailman/listinfo/molvis-list
> > > >>>
> > > >>
> > > >>
> > > >>_______________________________________________
> > > >>Molvis-list mailing list
> > > >> Molvis-list at bioinformatics.org
> > > >> https://bioinformatics.org/mailman/listinfo/molvis-list
> > > >>
> > > >
> > > >
> > > >
> > > >--
> > > >Keith McLaughlin
> > > >University of South Florida
> > > >Physics Dept. PHY225
> > > >4202 E. Fowler Ave
> > > >Tampa, FL 33620
> > > >_______________________________________________
> > > >Molvis-list mailing list
> > > > Molvis-list at bioinformatics.org
> > > > https://bioinformatics.org/mailman/listinfo/molvis-list
> > >
> > >
> > > --
> > > =====================================================
> > > Herbert J. Bernstein, Professor of Computer Science
> > > Dowling College, Kramer Science Center, KSC 121
> > > Idle Hour Blvd, Oakdale, NY, 11769
> > >
> > > +1-631-244-3035
> > > yaya at dowling.edu
> > > =====================================================
> > > _______________________________________________
> > > Molvis-list mailing list
> > > Molvis-list at bioinformatics.org
> > > https://bioinformatics.org/mailman/listinfo/molvis-list
> > >
> >
> >
> >
> > --
> > Keith McLaughlin
> > University of South Florida
> > Physics Dept. PHY225
> > 4202 E. Fowler Ave
> > Tampa, FL 33620
> >
>
>
>
> --
> Keith McLaughlin
> University of South Florida
> Physics Dept. PHY225
> 4202 E. Fowler Ave
> Tampa, FL 33620
>
--
Keith McLaughlin
University of South Florida
Department of Physics (PHY225)
4202 E. Fowler Ave
Tampa, FL 33620
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