[Dock-fans] execl: permission denied

Scott Brozell sbrozell at scripps.edu
Tue May 27 14:43:07 PDT 2008 

Hi,

We have added a FAQ for dms installation:

http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#dmsinstall

Scott

On Wed, 21 May 2008, Eric Pettersen wrote:

> When I run dms, I get the same output you did:
> 
> dms rec_noH.pdb -n -w 1.4 -v -o /dev/null
> 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)
> 
> So it looks like you're good to go!
> 
> --Eric
> 
> On May 21, 2008, at 2:05 PM, Teck Maan wrote:
> 
> > 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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