[sharp-discuss] installation error
Eugene Valkov
eugene.valkov at googlemail.com
Tue Jan 15 19:42:38 GMT 2008
Dear SHARP users & developers,
I've encountered an error during the installation of the Linux version of
the SHARP package.
The error occurs invariably as I execute the installSHARP script with or
without the -f flag.
I attach the full log of the install below.
[eugene at pokey SHARP]$ ./installSHARP -f
NOTE : You've choosen the "fast" installation option: most defaults
will be accepted without requesting a confirmation from you. If
things are not working properly afterwards, you might want to rerun
this script without this option.
###########################################################
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 19:37 .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
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_19:39:16"
===========================================================
========= 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 > no
---------------------------------------------------------
------- 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 : 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:/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:
ERROR : during host resources
I will be very grateful if anyone could shed light on this problem. The
system and the linux install is fairly new and clean. The architecture is
i386 with Athlon processor running FC7 Linux.
My most recent successful installation of SHARP on a dual core Intel-based
FC5 system went without a hitch and the two systems are very similar in
setup (at least to my knowledge) so I'm very puzzled by this.
Eugene
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