[Molvis-list] hardware upgrades to increase rasmol performance on
very large systems.
Keith McLaughlin
kmclaugh at physics.cas.usf.edu
Sun Apr 15 16:56:31 EDT 2007
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
More information about the Molvis-list
mailing list