[Dock-fans] execl: permission denied
Eric Pettersen
pett at cgl.ucsf.edu
Wed May 21 14:10:34 PDT 2008
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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