[sharp-discuss] installation error

Eugene Valkov eugene.valkov at googlemail.com
Tue Jan 15 20:51:23 GMT 2008


Hi Clemens,

You're absolutely correct!

I've typed "export LD_LIBRARY_PATH=/xtal/XtalView/lib/ibmpcLinux2" to 
avoid possible confusion with CCP4 setup and SHARP installed like a 
charm. I did have a look for all the directories in the path and 
/xtal/CCP4/ccp4-6.0.2/extralib appeared not to exist so I tried without it.

Many thanks to you and Claus for help!

(Logfile for installation is provided at the end of the email for those 
interested)

Eugene


Clemens Vonrhein wrote:
> Hi Eugene,
>
> each entry in LD_LIBRARY_PATH needs to exist - probably
>
>   /xtal/CCP4/ccp4-6.0.2/extralib
>
> is the culprit? this is from CCP4 default setup - it adds a
> non-existing directory ... 
>
> Cheers
>
> Clemens
>
> On Tue, Jan 15, 2008 at 08:28:40PM +0000, Eugene Valkov wrote:
>   
>> Hi Claus,
>>
>> This didn't work - error appears again (this time without the empty 
>> component "::")
>>
>> Any other thoughts? I'm sure this is something maddeningly simple - I 
>> just can't figure out what.
>>
>> Thanks,
>>
>> Eugene
>>
>> WARNING : invalid answer - try again.
>>
>> 4. list of directories for
>> LD_LIBRARY_PATH/DYLD_LIBRARY_PATH variable :
>> [/xtal/XtalView/lib/ibmpcLinux2:/xtal/EMAN/lib:/xtal/CCP4/ccp4-6.0.2/lib:/xtal/CCP4/ccp4-6.0.2/extralib] 
>>     
>> Claus Flensburg wrote:
>>
>>     
>>> Hi Eugene,
>>>
>>> On Tue, Jan 15, 2008 at 07:42:38PM +0000, Eugene Valkov wrote:
>>> ...
>>>  
>>>       
>>>>  4. list of directories for
>>>>     LD_LIBRARY_PATH/DYLD_LIBRARY_PATH variable :
>>>>     [/xtal/XtalView/lib/ibmpcLinux2:/xtal/EMAN/lib:/xtal/CCP4/ccp4-6.0.2
>>>> /lib::/xtal/CCP4/ccp4-6.0.2/extralib] >
>>>>
>>>>
>>>> WARNING : invalid answer - try again.
>>>>
>>>> /xtal/SHARP/adm/bin/dbtofile: line 284: warnnig: command not found
>>>>  4. list of directories for
>>>>     LD_LIBRARY_PATH/DYLD_LIBRARY_PATH variable :
>>>>     [/xtal/XtalView/lib/ibmpcLinux2:/xtal/EMAN/lib:/xtal/CCP4/ccp4-6.0.2
>>>> /lib::/xtal/CCP4/ccp4-6.0.2/extralib] >
>>>>
>>>>
>>>> The error message simply repeats regardless of input. As I enter Ctrl-C, 
>>>> the
>>>> following message is displayed:
>>>>    
>>>>         
>>> it appears the shell variable LD_LIBRARY_PATH has en empty component "::".
>>> The install script tests for and requires that each component exists.
>>>
>>> Try this:
>>>
>>> env 
>>> LD_LIBRARY_PATH=/xtal/XtalView/lib/ibmpcLinux2:/xtal/EMAN/lib:/xtal/CCP4/ccp4-6.0.2/lib:/xtal/CCP4/ccp4-6.0.2/extralib ./installSHARP -f
>>>
>>> Hope this helps.
>>>
>>>
>>> Regards,
>>>
>>> ClAuS
>>>
>>>  
>>>       
>> _______________________________________________
>> sharp-discuss mailing list
>> sharp-discuss at globalphasing.com
>> https://www.globalphasing.com/mailman/listinfo/sharp-discuss
>>
>>     

[eugene at pokey SHARP]$ export LD_LIBRARY_PATH=/xtal/XtalView/lib/ibmpcLinux2
[eugene at pokey SHARP]$ ./installSHARP


###########################################################

Welcome to the installation of SHARP/autoSHARP
and SUSHI


Copyright (C) 1999-2005 by Global Phasing Ltd.


Authors: Clemens Vonrhein & Eric Blanc

###########################################################


===========================================================
========= Section 1 : pre-installation checks
===========================================================

searching command sed: done


NOTE : everything ok!



NOTE : You are going to install SHARP/autoSHARP & SUSHI in the current
directory /xtal/SHARP.
This will be referred to as the $BDG_home directory.

Proceed ? [y]es/[n]o > y


NOTE : Previous version(s) of .bdgrc have been found:

-rw-r--r-- 1 eugene xtal 6772 2008-01-15 20:31 .bdgrc
-rw-r--r-- 1 eugene xtal 6772 2008-01-15 19:31 .bdgrc_20080115_19:31:45
-rw-r--r-- 1 eugene xtal 6772 2008-01-15 19:31 .bdgrc_20080115_19:37:25
-rw-r--r-- 1 eugene xtal 6772 2008-01-15 19:37 .bdgrc_20080115_19:39:16
-rw-r--r-- 1 eugene xtal 6772 2008-01-15 19:39 .bdgrc_20080115_20:21:13
-rw-r--r-- 1 eugene xtal 6772 2008-01-15 20:21 .bdgrc_20080115_20:23:53
-rw-r--r-- 1 eugene xtal 6772 2008-01-15 20:23 .bdgrc_20080115_20:30:27
-rw-r--r-- 1 eugene xtal 6772 2008-01-15 20:30 .bdgrc_20080115_20:31:43

Which one do you want to use as template (skip with '#') :
[.bdgrc] >

WARNING : The current directory /xtal/SHARP already
contains a SHARP/autoSHARP installation

Do you want to replace it ? [y]es/[n]o > y

SHARP site administrator e-mail :
[eugene.valkov at googlemail.com] >


===========================================================
========= Section 2 : installing SUSHI
===========================================================


WARNING : it seems that there is already a SUSHI
installation!

Do you want to overwrite this ? [y]es/[n]o/[e]xit/[s]kip > y

Absolute path to the compressed SUSHI file(s) ([s]kip) :
[/xtal/SHARP/sushi.tar.gz] >

extracting /xtal/SHARP/sushi.tar.gz ... done



===========================================================
========= Section 3 : installing SHARP
===========================================================


NOTE : Installation of binaries is not mandatory at this
point. Binaries installation can also be done when
adding new machines (via the "newmachine"
command).

Install SHARP binaries now ? [y]es/[n]o/[e]xit/[s]kip > y

Machine architecture ( linux ) :
[linux] >

WARNING : The directory "/xtal/SHARP/bin/linux_exe" is
already present. This may happen if you have
already installed SHARP or BUSTER. Should you
choose to install the new SHARP binaries, it will
overwrite the previous SHARP binaries, if they are
present in this directory.

Do you want to continue extracting binaries ? [y]es/[n]o/[e]xit/[s]kip > y

Absolute path to the compressed SHARP file(s) ([s]kip) :
[/xtal/SHARP/sharp.linux.tar.gz] >

extracting /xtal/SHARP/sharp.linux.tar.gz ... done



===========================================================
========= Section 4 : installing
===========================================================


NOTE : Tutorials are worked examples how to run
SHARP/autoSHARP through SUSHI. They use 1.2 MB of
disk space.

Do you want to install the tutorials now ? [y]es/[n]o/[e]xit/[s]kip > y

WARNING : The tutorials are already installed in
"/xtal/SHARP/samples"

Do you want to overwrite these ? [y]es/[n]o/[e]xit/[s]kip > y

Absolute path to the compressed tutorials file(s) ([s]kip) :
[/xtal/SHARP/sharp_tutorials.tar.gz] >

extracting /xtal/SHARP/sharp_tutorials.tar.gz ... done



===========================================================
========= Section 5 : installing HELPERS
===========================================================


---------------------------------------------------------
------- Section 5.1 : for client(s)
---------------------------------------------------------


NOTE : The helper applications are required to display maps
and various graphs directly from a web browser. You
may want to install them for each operating system
the SHARP users have access to.


NOTE : Do you want to install helpers applications for os

linux ? [y]es/[n]o > y

WARNING : there is/are already some client applications in
/xtal/SHARP/helpers/linux

Do you want to overwrite this ? [y]es/[n]o/[e]xit/[s]kip > y

Absolute path to the compressed client helpers file(s) ([s]kip) :
[/xtal/SHARP/helpers_client.linux.tar.gz] >

extracting /xtal/SHARP/helpers_client.linux.tar.gz ... done



---------------------------------------------------------
------- Section 5.2 : for server (http daemon)
---------------------------------------------------------


NOTE : The helpers applications for the server are required
for the SUSHI operation. To have a functional
installation, you need to install them on the server
machine.


NOTE : The only mandatory helper on the server side is the
Apache http daemon.

Do you want to install them ? [y]es/[n]o/[e]xit/[s]kip > y

WARNING : there is/are already some server applications in
/xtal/SHARP/helpers/linux

Do you want to overwrite this ? [y]es/[n]o/[e]xit/[s]kip > y

Absolute path to the compressed server helpers file(s) ([s]kip) :
[/xtal/SHARP/helpers_server.linux.tar.gz] >

extracting /xtal/SHARP/helpers_server.linux.tar.gz ... done


NOTE : saving existing file "/xtal/SHARP/.bdgrc" in
"/xtal/SHARP/.bdgrc_20080115_20:33:17"




===========================================================
========= Section 6 : CONFIGURATION
===========================================================


NOTE : If you had a previous version of
SHARP/autoSHARP running (in a different
directory) we can try to copy all necessary
configuration files over. However, this will only
work with fairly new versions of SUSHI. So if you
want to be on the safe side (especially if its your
first installation) you should say "no" here.


NOTE : You can only clone an older installation if that
installation already had pokey as a configured
machine.

Copy configuration from previous SHARP/autoSHARP installation ? 
[y]es/[n]o > n

---------------------------------------------------------
------- Section 6.1 : server setup
---------------------------------------------------------


NOTE : We will now generate a basic server setup file. Make
sure to answer the questions accurately - otherwise
the interface SUSHI may not work properly.


NOTE : You can re-configure your server by running
"host-setup".


NOTE : The SHARP / SUSHI server will be set to the machine
pokey

Continue ? [y]es/[n]o/[e]xit/[s]kip > y

NOTE : The operating system seems to be: Linux - release
2.6.23.12-52.fc7


NOTE : The computer chip appears to be : i686


NOTE : saving existing file
"/xtal/SHARP/machines/pokey/host.setup" in
"/xtal/SHARP/machines/pokey/host.setup_20080115_20:35:33"


NOTE : the defaults in the following section should be
adequate in most cases.


1. Location of temporary files (min 64 MB free) (absolute
path) :
[/tmp] >

2. Perl 5 location :
[/usr/bin/perl] >

3. Mailer program location (usually sendmail) :
[/usr/sbin/sendmail] >

4. list of directories for
LD_LIBRARY_PATH/DYLD_LIBRARY_PATH variable :
[/xtal/XtalView/lib/ibmpcLinux2] >

NOTE : copied the newly created file
/xtal/SHARP/machines/pokey/host.setup to
/xtal/SHARP/machines/host.setup. Any CLIENT for which
you haven't run the "host-setup" script will at least
pick up this setup.


---------------------------------------------------------
------- Section 6.2 : CCP4 setup
---------------------------------------------------------


NOTE : We will now generate a basic CCP4 setup file. Make
sure to answer the questions accurately - otherwise
most of the helper applications needed to view the
SHARP/autoSHARP results won't work. You can accept
the presented defaults by hitting the "Return" key


NOTE : You can re-configure CCP4 by running
"ccp4-setup".

Continue ? [y]es/[n]o/[e]xit/[s]kip > y

NOTE : the defaults in the following section should be
adequate in most cases.


1. root directory of CCP4 installation (absolute path) :
[/xtal/CCP4/ccp4-6.0.2] >

2. scratch directory for CCP4 programs (absolute path) :
[/tmp/eugene] >

3. CCP4 directory with X11 subdirectory and font data
(absolute path) :
[/xtal/CCP4/ccp4-6.0.2/lib] >

4. CCP4 directory with 'environ.def' and 'default.def'
(absolute path) :
[/xtal/CCP4/ccp4-6.0.2/include] >

5. CCP4 directory with 'symop.lib' and 'atomsf.lib' (and
maybe syminfo.lib) (absolute path) :
[/xtal/CCP4/ccp4-6.0.2/lib/data] >

6. CCP4 directory with executables (absolute path) :
[/xtal/CCP4/ccp4-6.0.2/bin] >

7. location of 'font84.dat' file (absolute path) :
[/xtal/CCP4/ccp4-6.0.2/lib/font84.dat] >

8. scratch directory for CCP4 'binsort' program (absolute
path) :
[/tmp/eugene] >

9. location of the mmcif dictionary file (absolute path) :
[/xtal/CCP4/ccp4-6.0.2/lib/cif_mmdic.lib] >

10. CCP4 directory containing shared libraries (absolute
path) :
[/xtal/CCP4/ccp4-6.0.2/lib] >


NOTE : copied the newly created file
/xtal/SHARP/machines/pokey/ccp4.setup to
/xtal/SHARP/machines/ccp4.setup. Any MASTER for which
you haven't run the "ccp4-setup" script will at least
pick up this setup.


---------------------------------------------------------
------- Section 6.3 : SHELX setup
---------------------------------------------------------


NOTE : We will now generate a basic SHELX setup file. Make
sure to answer the questions accurately - otherwise
the use of SHELXC/SHELXD for the detection of heavy
atom substructures won't work. You can accept the
presented defaults by hitting the "Return" key. If
you don't have SHELX and are not planning to use it
for heavy atom detection you should give the name of
any directory (e.g. /tmp).


NOTE : You can re-configure SHELX by running
"shelx-setup".

Continue ? [y]es/[n]o/[e]xit/[s]kip > y

NOTE : the defaults in the following section should be
adequate in most cases.


1. Path to SHELX binaries (absolute path) :
[/xtal/shelx] >

NOTE : copied the newly created file
/xtal/SHARP/machines/pokey/shelx.setup to
/xtal/SHARP/machines/shelx.setup. Any MASTER for
which you haven't run the "shelx-setup" script will
at least pick up this setup.


---------------------------------------------------------
------- Section 6.4 : mapman setup
---------------------------------------------------------


NOTE : We will now generate a basic mapman setup file. Make
sure to answer the questions accurately - otherwise
some of the helper applications needed to view the
SHARP results won't work. You can accept the
presented defaults by hitting the "Return" key. If
you don't have mapman installed and are not planning
to view results with O you should give the name of
any binary (e.g. /bin/false) - since it is only used
to generate bones files.


NOTE : You can re-configure mapman by running
"mapman-setup".

Continue ? [y]es/[n]o/[e]xit/[s]kip > y

NOTE : the defaults in the following section should be
adequate in most cases.


1. Path to mapman (absolute path) :
[/xtal/usf/mapman] >

NOTE : copied the newly created file
/xtal/SHARP/machines/pokey/mapman.setup to
/xtal/SHARP/machines/mapman.setup. Any CLIENT for
which you haven't run the "mapman-setup" script will
at least pick up this setup.


---------------------------------------------------------
------- Section 6.5 : XtalView setup
---------------------------------------------------------


NOTE : We will now generate a basic XtalView setup file.
Make sure to answer the questions accurately -
otherwise some of the helper applications needed to
view the SHARP results won't work. You can accept the
presented defaults by hitting the "Return" key. If
you don't have XtalView installed and are not
planning to view results with XFit you should give
the name of any directory (e.g. /tmp) - since it is
only used to generate ridge-line files.


NOTE : You can re-configure XtalView by running
"xtalview-setup".

Continue ? [y]es/[n]o/[e]xit/[s]kip > y

NOTE : the defaults in the following section should be
adequate in most cases.


1. Path to XtalView installation (absolute path) :
[/xtal/XtalView] >

NOTE : copied the newly created file
/xtal/SHARP/machines/pokey/xtalview.setup to
/xtal/SHARP/machines/xtalview.setup. Any CLIENT for
which you haven't run the "xtalview-setup" script
will at least pick up this setup.


---------------------------------------------------------
------- Section 6.6 : httpd setup
---------------------------------------------------------


NOTE : We will now generate a configuration file for the
Apache httpd. You can either use the "httpd" binary
from the "helper applications" page on our WWW server
or your own binary. In the latter case the generated
configuration file requires version 1.3.28 or higher.


NOTE : You can re-configure the Apache httpd by running
"httpd-setup".

Continue [y]es/[n]o/[e]xit/[s]kip > y

NOTE : the defaults in the following section should be
adequate in most cases.


1. Location of the http daemon (incl. program name) :
[/xtal/SHARP/helpers/linux/httpd.glibc23] >

2. Communication port for server :
[8080] >

NOTE : saving existing file
"/xtal/SHARP/sushi/base/.sharpaccess.pokey.8080" in
"/xtal/SHARP/sushi/base/.sharpaccess.pokey.8080_20080115_20:36:54"


NOTE : saving existing file
"/xtal/SHARP/sushi/cgi-bin/.sharpaccess.pokey.8080"
in
"/xtal/SHARP/sushi/cgi-bin/.sharpaccess.pokey.8080_20080115_20:36:54"


NOTE : saving existing file
"/xtal/SHARP/sushi/.sharpaccess.pokey.8080" in
"/xtal/SHARP/sushi/.sharpaccess.pokey.8080_20080115_20:36:54"


NOTE : saving existing file
"/xtal/SHARP/users/.sharpaccess.pokey.8080" in
"/xtal/SHARP/users/.sharpaccess.pokey.8080_20080115_20:36:54"


NOTE : creating apropriate link for AstexViewer
(sushi/base/tmp -> /tmp)


NOTE : The http deamon is now installed and configured.

Do you want to start the httpd now ? [y]es/[n]o > y

ERROR : A http daemon appears to be running already. Or
maybe the server was not properly shut down. If this
is the case, the lock file
/xtal/SHARP/sushi/logs/httpd.pid must be removed
before restarting the server. The easiest way of
doing this is to run the "kill_server" command.


Checking if it's running:

A SUSHI server is running on

pokey:8080


---------------------------------------------------------
------- Section 6.7 : helper applications setup
---------------------------------------------------------


NOTE : We will now generate a basic bin/helpers.local file
- based purely on your current environment. This file
is only used when viewing results (maps, models,
plots) through the httpd server. You can add
configuration for more machines to this file, by
running adm/bin/helpers-setup on this other machine.
If you want to edit it, please read the notes at the
top of the file. Another example file is given in the
file bin/helpers.local_template.

Continue ? [y]es/[n]o/[e]xit/[s]kip > y

---------------------------------------------------------
------- Section 6.8 : permission setting
---------------------------------------------------------


NOTE : We adjust permissions for some directories/files
based on your current umask (0022) to mode "all".
This way the intended audience of users can access
them. You can always change this using the
perm-setup administrative command.


Setting permissions for SHARP to mode "all" ... done


---------------------------------------------------------
------- Section 6.9 : final SERVER setup
---------------------------------------------------------


NOTE : saving existing file "/xtal/SHARP/sushi/base/.bdgrc"
in "/xtal/SHARP/sushi/base/.bdgrc_20080115_20:37:05"


NOTE : saving existing file
"/xtal/SHARP/sushi/cgi-bin/.bdgrc" in
"/xtal/SHARP/sushi/cgi-bin/.bdgrc_20080115_20:37:05"


NOTE : You should be set up to use SUSHI.

To use SHARP, you must configure MASTER machines to
run SHARP binaries. You can do this using the
'newmachine' script.

You can add SHARP users to the database by using the
'newuser' script.

To use those administrative script (and many more),
you might want to make sure that
"/xtal/SHARP/adm/bin" is in your path, and that the
environment variable "BDG_home" is set to
"/xtal/SHARP". You can do this by setting:

in csh/tcsh (see example file 'setup.csh'):
setenv BDG_home /xtal/SHARP
set path = ( $BDG_home/adm/bin $path )

in sh/ksh/bash (see example file 'setup.sh'):
BDG_home=/xtal/SHARP
export BDG_home
PATH="${BDG_home}/adm/bin:$PATH"

NOTE : You can see a summary of commands available to the
SHARP site administrator by typing
"/xtal/SHARP/adm/bin/bdg-help".

grep: setup.sh: No such file or directory
./installSHARP: line 2405: [: -eq: unary operator expected
grep: setup.csh: No such file or directory
./installSHARP: line 2423: [: -eq: unary operator expected

NOTE : Installation completed






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