[Molvis-list] hardware upgrades to increase rasmol performance on
very large systems.
Keith McLaughlin
kmclau at gmail.com
Thu May 24 17:53:07 EDT 2007
Sorry. the beginning of the code was truncated. Here are the leading lines.
#include <stdlib.h>
#include <stdio.h>
#define REALYL double
//#define DEBUG
typedef struct {
On 5/24/07, Keith McLaughlin <kmclau at gmail.com> wrote:
>
> 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
>
--
Keith McLaughlin
University of South Florida
Department of Physics (PHY225)
4202 E. Fowler Ave
Tampa, FL 33620
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