[Dock-fans] execl: permission denied
Teck Maan
teck.m.lim at wmich.edu
Wed May 21 14:05:03 PDT 2008
Hi Eric
It think it works. But i am not sure if it is really working. Can i do a
quick check with you? After compiling, the directory where you install
(home/tkmaan/Desktop/dms/bin), contains only the dms (executable) and in
the directory (home/tkmaan/Desktop/dms/lib/dms/) only contains dmsd
dms_servers.proto and radii and man/man1 contains only dms.1? And if i
did a compile with rec_noH.pdb,
[tkmaan at roam98-105 bin]$ ./dms rec_noH.pdb -n -w 1.4 -v -o rec.ms
2317 atoms
S 11
O 444
N 389
C 1473
Servers initialized
Neighbors computed
Probes computed
Neighbors sent
Surface computed
Server request count:
localhost 87517
64657 points (19440 contact, 45217 reentrant)
11945.61 sq. A (3791.43 contact, 8154.17 reentrant)
5.41 pts/sq.A (5.13 contact, 5.55 reentrant)
It has no error. I suppose i have everything set correctly? Again, thank
you so much for your time and patience.
Teck Maan
On Wed, 2008-05-21 at 13:15 -0700, Eric Pettersen wrote:
> Hi Teck,
> You need to point LIBDIR and BINDIR to directories that actually
> exist. /usr/local does not exist by default on a Mac, much less /usr/
> local/lib and /usr/local/bin. Either you can create these
> directories or you can make some additional directories on your
> Desktop and point LIBDIR and BINDIR to those. If you decide to
> create the /usr/local directories, you will probably have to have
> admin privileges to do so, and you would want to ensure that the
> directories were writable by you (e.g. "sudo chown -R tkmaan /usr/
> local").
>
> --Eric
>
> On May 21, 2008, at 12:37 PM, Teck Maan wrote:
>
> > Hi Eric,
> > I decided to redo the installation again. So i unpack dms into my
> > desktop (home/Desktop/dms) and went from there. i did a shar then make
> > install. The GNUmakefile has LIBDIR = /usr/local/lib and BINDIR
> > = /usr/local/bin. The following is what i have.
> >
> > cd libpdb ; make OPT="-O"
> > make[1]: Entering directory `/home/tkmaan/Desktop/dms/libpdb'
> > cc -O -c -o pdb_read.o pdb_read.c
> > cc -O -c -o pdb_sprntf.o pdb_sprntf.c
> > cc -O -c -o pdb_sscanf.o pdb_sscanf.c
> > cc -O -c -o pdb_write.o pdb_write.c
> > cc -O -c -o pdbrun.o pdbrun.c
> > cc -O -c -o ms.o ms.c
> > ar cru libpdb.a pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o
> > pdbrun.o ms.o
> > ranlib libpdb.a
> > make[1]: Leaving directory `/home/tkmaan/Desktop/dms/libpdb'
> > cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
> > \"/usr/local/lib/dms/dmsd\" -Ilibpdb -O -c -o compute.o compute.c
> > cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
> > \"/usr/local/lib/dms/dmsd\" -Ilibpdb -O -c -o fwritev.o fwritev.c
> > cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
> > \"/usr/local/lib/dms/dmsd\" -Ilibpdb -O -c -o input.o input.c
> > cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
> > \"/usr/local/lib/dms/dmsd\" -Ilibpdb -O -c -o ms.o ms.c
> > cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
> > \"/usr/local/lib/dms/dmsd\" -Ilibpdb -O -c -o output.o output.c
> > cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
> > \"/usr/local/lib/dms/dmsd\" -Ilibpdb -O -c -o emalloc.o emalloc.c
> > cc -DDESTLIB=\"/usr/local/lib/dms/\" -DSERVER_PATH=
> > \"/usr/local/lib/dms/dmsd\" -Ilibpdb -O -c -o tokenize.o tokenize.c
> > cc -Llibpdb -o dms compute.o fwritev.o input.o ms.o output.o emalloc.o
> > tokenize.o -lpdb
> > rm -f /usr/local/man/man1/dms.1
> > cp dms.1 /usr/local/man/man1
> > cp: cannot create regular file `/usr/local/man/man1': No such file or
> > directory
> > make: *** [maninstall] Error 1
> >
> > I have no idea why it cannot create /usr/local/man/man1. So i compile
> > the rec_noH.pdb
> >
> > [tkmaan at roam98-105 dms]$ ./dms rec_noH.pdb -n -w 1.4 -v -o rec.ms
> > 2317 atoms
> > /usr/local/lib/dms/radii: No such file or directory
> >
> > So i delete the "proto" in the radii.proto (in home/Desktop/dms) and
> > compile again.
> >
> > [tkmaan at roam98-105 dms]$ ./dms rec_noH.pdb -n -w 1.4 -v -o rec.ms
> > 2317 atoms
> > S 11
> > O 444
> > N 389
> > C 1473
> > execl: No such file or directory
> >
> > and i got no such file or directory error instead of permission
> > denied.
> > few things i do not get it is that, i unpack my shar files in my
> > home/Desktop/dms directory, and do a "make install". I
> > checked /usr/local/lib/ and usr/local/bin directory, i do not see any
> > file being created. In fact, files are compiled and put into my
> > home/Desktop/dms directory. I believe this usr/local/lib and
> > usr/local/bin must be pointing to the same directory. So i am just
> > wondering now how do to fix this "no such file or directory" error.
> > Thanks.
> >
> > Teck Maan
> >
> >
> >
> > On Wed, 2008-05-21 at 11:23 -0700, Eric Pettersen wrote:
> >> Hi Teck,
> >> You've duplicated the error described in this message:
> >>
> >> http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2007-
> >> February/
> >> 000920.html
> >>
> >> Basically, you can't edit the GNUmakefile to have the LIBDIR/BINDIR
> >> variables point to the same place where the source is. You need to
> >> edit the GNUmakefile, change those variables, and recompile.
> >>
> >> --Eric
> >>
> >> On May 21, 2008, at 11:13 AM, Teck Maan wrote:
> >>
> >>> Hi Eric,
> >>> I checked my dmsd folder. It is there. It contains 7 items.
> >>> 1. emalloc.c
> >>> 2. freadv.c
> >>> 3.GNUmakefile
> >>> 4. lookat.c
> >>> 5. server.c
> >>> 6. test.pdb
> >>> 7. viewat.c
> >>>
> >>> and the folder /home/tkmaan/Desktop/dms, does exist. and i execute
> >>> the
> >>> dms program using the following command: ./dms rec_noH.pdb -n -w
> >>> 1.4 -v
> >>> -o rec.ms. i am just stucked at execl line where the permission is
> >>> denied. I tried su, same error. Any thought?
> >>>
> >>> Teck Maan
> >>> On Tue, 2008-05-20 at 16:32 -0700, Eric Pettersen wrote:
> >>>>> cc -DDESTLIB=\"/home/tkmaan/Desktop/dms/\" -DSERVER_PATH=
> >>>>> \"/home/tkmaan/Desktop/dms/dmsd\" -Ilibpdb -O -c -o tokenize.o
> >>>>> tokenize.c
> >>>>> cc -Llibpdb -o dms compute.o fwritev.o input.o ms.o output.o
> >>>>> emalloc.o
> >>>>> tokenize.o -lpdb
> >>>>> rm -f /home/tkmaan/Desktop/man/man1/dms.1
> >>>>> cp dms.1 /home/tkmaan/Desktop/man/man1
> >>>>> cp: cannot create regular file `/home/tkmaan/Desktop/man/man1': No
> >>>>> such
> >>>>> file or directory
> >>>>> make: *** [maninstall] Error 1
> >>>>> [root at localhost dms]# ./dms rec_noH.pdb -n -w 1.4 -v -o rec.ms
> >>>>> 2317 atoms
> >>>>> S 11
> >>>>> O 444
> >>>>> N 389
> >>>>> C 1473
> >>>>> execl: Permission denied
> >>>>
> >>>> Hi Teck,
> >>>> The error indicates that /home/tkmaan/Desktop/dms/dmsd cannot be
> >>>> executed. Check that the folder /home/tkmaan/Desktop/dms exists.
> >>>> Check that the file dmsd exists in that folder. Check that the
> >>>> file
> >>>> is executable.
> >>>>
> >>>>
> >>>> --Eric
> >>>>
> >>>>
> >>>> Eric Pettersen
> >>>>
> >>>> UCSF Computer Graphics Lab
> >>>>
> >>>> http://www.cgl.ucsf.edu
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Dock-fans mailing list
> >>>> Dock-fans at docking.org
> >>>> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >>>
> >>
> >
>
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