Dear SHARP users & developers,<br><br>I've encountered an error during the installation of the Linux version of the SHARP package.<br><br>The error occurs invariably as I execute the installSHARP script with or without the -f flag.
<br><br>I attach the full log of the install below.<br><br>[eugene@pokey SHARP]$ ./installSHARP -f<br> <br> <br> NOTE : You've choosen the "fast" installation option: most defaults<br> will be accepted without requesting a confirmation from you. If
<br> things are not working properly afterwards, you might want to rerun<br> this script without this option.<br> <br> <br> ########################################################### <br> <br> Welcome to the installation of SHARP/autoSHARP
<br> and SUSHI <br> <br> <br> Copyright (C) 1999-2005 by Global Phasing Ltd.<br> <br> <br> Authors: Clemens Vonrhein & Eric Blanc<br> <br> ###########################################################
<br> <br> <br> ===========================================================<br> ========= Section 1 : pre-installation checks<br> ===========================================================<br> <br> searching command sed: done
<br> <br> <br> NOTE : everything ok!<br> <br> <br> <br> NOTE : You are going to install SHARP/autoSHARP & SUSHI in the current<br> directory /xtal/SHARP. <br> This will be referred to as the $BDG_home directory.
<br> <br> Proceed ? [y]es/[n]o > y<br> <br> <br> NOTE : Previous version(s) of .bdgrc have been found:<br> <br> -rw-r--r-- 1 eugene xtal 6772 2008-01-15 19:37 .bdgrc<br> -rw-r--r-- 1 eugene xtal 6772 2008-01-15 19:31 .bdgrc_20080115_19:31:45
<br> -rw-r--r-- 1 eugene xtal 6772 2008-01-15 19:31 .bdgrc_20080115_19:37:25<br> <br> Which one do you want to use as template (skip with '#') :<br> [.bdgrc] > <br> <br> WARNING : The current directory /xtal/SHARP already
<br> contains a SHARP/autoSHARP installation<br> <br> Do you want to replace it ? [y]es/[n]o > y<br> <br> SHARP site administrator e-mail :<br> [<a href="mailto:eugene.valkov@googlemail.com">
eugene.valkov@googlemail.com</a>] > <br> <br> <br> ===========================================================<br> ========= Section 2 : installing SUSHI<br> ===========================================================
<br> <br> <br> WARNING : it seems that there is already a SUSHI<br> installation!<br> <br> Do you want to overwrite this ? [y]es/[n]o/[e]xit/[s]kip > y<br> <br> Absolute path to the compressed SUSHI file(s) ([s]kip) :
<br> [/xtal/SHARP/sushi.tar.gz] > <br> <br> extracting /xtal/SHARP/sushi.tar.gz ... done<br> <br> <br> <br> ===========================================================<br> ========= Section 3 : installing SHARP
<br> ===========================================================<br> <br> <br> NOTE : Installation of binaries is not mandatory at this<br> point. Binaries installation can also be done when<br> adding new machines (via the "newmachine"
<br> command).<br> <br> Install SHARP binaries now ? [y]es/[n]o/[e]xit/[s]kip > y<br> <br> Machine architecture ( linux ) :<br> [linux] > <br> <br> WARNING : The directory "/xtal/SHARP/bin/linux_exe" is
<br> already present. This may happen if you have<br> already installed SHARP or BUSTER. Should you<br> choose to install the new SHARP binaries, it will<br> overwrite the previous SHARP binaries, if they are
<br> present in this directory.<br> <br> Do you want to continue extracting binaries ? [y]es/[n]o/[e]xit/[s]kip > y<br> <br> Absolute path to the compressed SHARP file(s) ([s]kip) :<br> [/xtal/SHARP/sharp.linux.tar.gz] >
<br> <br> extracting /xtal/SHARP/sharp.linux.tar.gz ... done<br> <br> <br> <br> ===========================================================<br> ========= Section 4 : installing <br> ===========================================================
<br> <br> <br> NOTE : Tutorials are worked examples how to run<br> SHARP/autoSHARP through SUSHI. They use 1.2 MB of<br> disk space.<br> <br> Do you want to install the tutorials now ? [y]es/[n]o/[e]xit/[s]kip > y
<br> <br> WARNING : The tutorials are already installed in<br> "/xtal/SHARP/samples"<br> <br> Do you want to overwrite these ? [y]es/[n]o/[e]xit/[s]kip > y<br> <br> Absolute path to the compressed tutorials file(s) ([s]kip) :
<br> [/xtal/SHARP/sharp_tutorials.tar.gz] > <br> <br> extracting /xtal/SHARP/sharp_tutorials.tar.gz ... done<br> <br> <br> <br> ===========================================================<br> ========= Section 5 : installing HELPERS
<br> ===========================================================<br> <br> <br> ---------------------------------------------------------<br> ------- Section 5.1 : for client(s)<br> ---------------------------------------------------------
<br> <br> <br> NOTE : The helper applications are required to display maps<br> and various graphs directly from a web browser. You<br> may want to install them for each operating system<br> the SHARP users have access to.
<br> <br> <br> NOTE : Do you want to install helpers applications for os<br> <br> linux ? [y]es/[n]o > y<br> <br> WARNING : there is/are already some client applications in<br> /xtal/SHARP/helpers/linux
<br> <br> Do you want to overwrite this ? [y]es/[n]o/[e]xit/[s]kip > y<br> <br> Absolute path to the compressed client helpers file(s) ([s]kip) :<br> [/xtal/SHARP/helpers_client.linux.tar.gz] >
<br> <br> extracting /xtal/SHARP/helpers_client.linux.tar.gz ... done<br> <br> <br> ---------------------------------------------------------<br> ------- Section 5.2 : for server (http daemon)<br> ---------------------------------------------------------
<br> <br> <br> NOTE : The helpers applications for the server are required<br> for the SUSHI operation. To have a functional<br> installation, you need to install them on the server<br> machine.<br> <br>
<br> NOTE : The only mandatory helper on the server side is the<br> Apache http daemon.<br> <br> Do you want to install them ? [y]es/[n]o/[e]xit/[s]kip > y<br> <br> WARNING : there is/are already some server applications in
<br> /xtal/SHARP/helpers/linux<br> <br> Do you want to overwrite this ? [y]es/[n]o/[e]xit/[s]kip > y<br> <br> Absolute path to the compressed server helpers file(s) ([s]kip) :<br> [/xtal/SHARP/helpers_server.linux.tar.gz] >
<br> <br> extracting /xtal/SHARP/helpers_server.linux.tar.gz ... done<br> <br> <br> NOTE : saving existing file "/xtal/SHARP/.bdgrc" in<br> "/xtal/SHARP/.bdgrc_20080115_19:39:16"<br> <br>
<br> <br> ===========================================================<br> ========= Section 6 : CONFIGURATION<br> ===========================================================<br> <br> <br> NOTE : If you had a previous version of
<br> SHARP/autoSHARP running (in a different<br> directory) we can try to copy all necessary<br> configuration files over. However, this will only<br> work with fairly new versions of SUSHI. So if you
<br> want to be on the safe side (especially if its your<br> first installation) you should say "no" here.<br> <br> <br> NOTE : You can only clone an older installation if that<br> installation already had pokey as a configured
<br> machine.<br> <br> Copy configuration from previous SHARP/autoSHARP installation ? [y]es/[n]o > no<br> <br> ---------------------------------------------------------<br> ------- Section 6.1 : server setup
<br> ---------------------------------------------------------<br> <br> <br> NOTE : We will now generate a basic server setup file. Make<br> sure to answer the questions accurately - otherwise<br> the interface SUSHI may not work properly.
<br> <br> <br> NOTE : You can re-configure your server by running<br> "host-setup".<br> <br> <br> NOTE : The SHARP / SUSHI server will be set to the machine<br> pokey<br> <br> Continue ? [y]es/[n]o/[e]xit/[s]kip > y
<br> <br> NOTE : The operating system seems to be: Linux - release<br> 2.6.23.12-52.fc7<br> <br> <br> NOTE : The computer chip appears to be : i686<br> <br> <br> NOTE : the defaults in the following section should be
<br> adequate in most cases.<br> <br> <br> 1. Location of temporary files (min 64 MB free) (absolute<br> path) :<br> [/tmp] > <br> <br> 2. Perl 5 location :<br> [/usr/bin/perl] > <br> <br> 3. Mailer program location (usually sendmail) :
<br> [/usr/sbin/sendmail] > <br> <br> 4. list of directories for<br> LD_LIBRARY_PATH/DYLD_LIBRARY_PATH variable :<br> [/xtal/XtalView/lib/ibmpcLinux2:/xtal/EMAN/lib:/xtal/CCP4/ccp4-6.0.2/lib::/xtal/CCP4/ccp4-
6.0.2/extralib] > <br><br><br>WARNING : invalid answer - try again.<br> <br>/xtal/SHARP/adm/bin/dbtofile: line 284: warnnig: command not found<br> 4. list of directories for<br> LD_LIBRARY_PATH/DYLD_LIBRARY_PATH variable :
<br> [/xtal/XtalView/lib/ibmpcLinux2:/xtal/EMAN/lib:/xtal/CCP4/ccp4-6.0.2/lib::/xtal/CCP4/ccp4-6.0.2/extralib] > <br><br><br>The error message simply repeats regardless of input. As I enter Ctrl-C, the following message is displayed:
<br><br><br> ERROR : during host resources<br><br><br><br>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.
<br><br>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.<br>
<br><br>Eugene<br><br> <br>