[Molvis-list] hardware upgrades to increase rasmol performance on
very large systems.
Keith McLaughlin
kmclaugh at physics.cas.usf.edu
Sun Apr 15 17:56:43 EDT 2007
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
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