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WebMO Support Forum » WebMO Installation » Initial Configuration of WebMO » Is there a comprehensive WebMO installation manual like manual for MOPAC for newbie/beginner ? « Previous Next »

Author Message
Anonymous
Posted on Monday, December 20, 2004 - 2:55 pm:   

Can somebody help i need to install webmo on local server, so computers inside the network can access webmo, while the computer outside the lab cannot access webmo.
I have tried to install WebMO several times and never succeed.

First, I installed it from user, and the error message that they could not create the directory for me automatically.

Then I ignore the warning message and install as root. Installation process went well, but I don't understand quite a lot from the first term. The script detected the server name, right ? In my case it is localhost.localdomain.

And next it asked me some questions regarding where to put the directory and specifying web path. I have started httpd, and I suppose specifying any location for the directory, except cgi-bin is fine.

However still did not work, ..
this is the error page from login.cgi
********************************************
Software error:

Invalid filehandle errorLog

For help, please send mail to the webmaster (root@localhost), giving this error message and the time and date of the error.
Software error:

[Tue Dec 21 03:07:24 2004] login.cgi: Invalid filehandle errorLog
Compilation failed in require at /var/www/cgi-bin/webmo/login.cgi line 17.

For help, please send mail to the webmaster (root@localhost), giving this error message and the time and date of the error.
************************************

this is the diagnose.html file

WebMO Diagnostic Output

The following information can be used to diagnose WebMO configuration problems.
Any failures will be marked in red.

System Information
Linux localhost.localdomain 2.6.9-1.667 #1 Tue Nov 2 14:41:25 EST 2004 i686 i686 i386 GNU/Linux

Checking Home Directory
Checking home directory: Failed
Home directory must be world-executable if WebMO is installed there

Checking CGI Directory
Checking /var/www/cgi-bin: Passed( 0755, root )
Checking /var/www/cgi-bin/login.cgi: Passed( 0755, root )
Checking /var/www/cgi-bin/interfaces: Passed( 0777, root )
Checking /var/www/cgi-bin/interfaces/globals.int: Passed( 0777, root )

Checking User Directory
Checking /root/webmo: Passed( 0777, root )
Checking /root/webmo/jobs: Passed( 0777, root )
Checking /root/webmo/users: Passed( 0777, root )
Checking /root/webmo/queue: Passed( 0777, root )
Checking /root/webmo/errors: Passed( 0777, root )

Checking Scratch Directory
Checking /tmp/webmo: Passed( 0777, jimmy )

Checking Apache Configuration
Checking for AddHandler cgi-scripts enabled: Passed
Checking for UserDir enabled: Passed
Checking for suExec enabled: Enabled
Apache is running as user apache
Document root directory is /var/www/html
Script alias directory is /var/www/cgi-bin/ (URL: /cgi-bin/)

WebMO Configuration File
backgroundGraphic="background_dna.gif"
catPath="/bin/cat"
cgiBase="/var/www/cgi-bin"
cpPath="/bin/cp"
externalBatchQueue=""
host="localhost.localdomain"
htmlBase="/var/www/html"
killPath="/bin/kill"
license="0405-2302-9833"
mkdirPath="/bin/mkdir"
mvPath="/bin/mv"
owner="Computational Chemistry on the WWW"
perlPath="/usr/bin/perl"
psOptions="-ef"
psPath="/bin/ps"
psRegExp="(\$pid, \$ppid, \$cpu_time) = /.{7}(.{7})(.{6}).{3}.{6}.{6}(.{12}).*/"
rcpPath="/usr/bin/rcp"
rmPath="/bin/rm"
rshPath="/usr/bin/rsh"
scpOptions="-o Protocol=1"
scpPath="/usr/bin/scp"
sendmailOptions="-t"
sendmailPath="/usr/sbin/sendmail"
servers="localhost.localdomain,0"
sshOptions="-o Protocol=1"
sshPath="/usr/bin/ssh"
systemScratch="/tmp"
tableBackgroundColor="#99cccc"
tarOptions="cf"
tarPath="/bin/tar"
unamePath="/bin/uname"
url_cgiBase="/webmo"
url_htmlBase="/webmo"
userBase="/root/webmo"
version="5.0.009"
webserver="autodetect"
whereisPath="/usr/bin/whereis"
schmidt
Posted on Monday, December 20, 2004 - 3:15 pm:   

You can find a step by step guide to installing WebMO at:
https://www.webmo.net/support/installation.html

However, the problem that you are experiencing is rather subtle. You have chosen to install WebMO in the system wide cgi-bin directory, as opposed into a user home directory. This is probably not the ideal choice on a Linux system, but it's certainly not a problem.

The problem is that you have chosen to install the WebMO user directory under the user 'root' home directory (/root). By default on Linux, only root can access this directory! Thus, when the webserver tries to access these files, permission is denied and WebMO dies with an error.

I would recommend reinstalling, and choosing a different location for the webmo user directory. Other than that, your configuration looks great.

If you want to install WebMO as a normal user, then you must install it in your personal public_html directory. For example,
/home/schmidt/public_html/webmo. You should basically be able to just follow the suggestions given by the installer.

Let me know if you have any further problems, and I will be happy to help you get set up.
jimmylawrence
Posted on Monday, December 20, 2004 - 3:40 pm:   

Thanks for your quick reply.

In fact, I installed WebMO based on instructions from the page. Still, I still get confused with the file things, since I am just a Linux newbie.

I am trying to access the login page from Firefox as root though..

Do you have a kind (or can you give more deep )of step-by-step instruction, especially for step 6 ?
There are several problems here :
If I login as user, the perl setup.pl command will show error message during installation.

If I follow the example path, when I installed as user then error message will appear, saying that it could not create that directory although I have inputted "y" on "create the directory ?" question.

Step 6 is a bit confusing for a beginner like me.

Can you help me with clean installation as user ?
Thank you in advance
jimmylawrence
Posted on Monday, December 20, 2004 - 3:55 pm:   

Another question:
how to uninstall webmo clean so that the files installed during those error won't affect the new ones ?

I am hoping that the rpm version of WebMO is available. But do you have plan to release the rpm version ?
jimmylawrence
Posted on Monday, December 20, 2004 - 4:07 pm:   

I have tried to reinstall it, however the software error; message still appears.

********************************************
Software error:

Invalid filehandle errorLog

For help, please send mail to the webmaster (root@localhost), giving this error message and the time and date of the error.
Software error:

[Tue Dec 21 04:29:05 2004] login.cgi: Invalid filehandle errorLog
Compilation failed in require at /var/www/cgi-bin/webmo/login.cgi line 17.

For help, please send mail to the webmaster (root@localhost), giving this error message and the time and date of the error.
************************************
Hurenkamp
Posted on Friday, July 22, 2005 - 8:00 am:   

I have the same problem, running Redhat 4 AS.

First I could not get the script to run at all, that turned out to be suexec, after turning that off the script runs in apache but I get the following error:

--
Software error:

Invalid filehandle errorLog

For help, please send mail to the webmaster (@), giving this error message and the time and date of the error.
Software error:

[Fri Jul 22 13:10:57 2005] login.cgi: Invalid filehandle errorLog
Compilation failed in require at /home/webmo/public_html/cgi-bin/webmo/login.cgi line 17.

For help, please send mail to the webmaster (@), giving this error message and the time and date of the error.
--

My diagnostic looks like this:

--
WebMO Diagnostic Output

The following information can be used to diagnose WebMO configuration problems.
Any failures will be marked in red.

System Information
Linux omac110 2.6.9-11.ELsmp #1 SMP Fri May 20 18:26:27 EDT 2005 i686 i686 i386 GNU/Linux

Checking Home Directory
Checking home directory: Passed

Checking CGI Directory
Checking /home/webmo/public_html/cgi-bin/webmo: Passed( 0755, webmo )
Checking /home/webmo/public_html/cgi-bin/webmo/login.cgi: Passed( 0755, webmo )
Checking /home/webmo/public_html/cgi-bin/webmo/interfaces: Passed( 0777, webmo )
Checking /home/webmo/public_html/cgi-bin/webmo/interfaces/globals.int:Passed( 0777, webmo )

Checking User Directory
Checking /home/webmo/webmo: Passed( 0777, webmo )
Checking /home/webmo/webmo/jobs: Passed( 0777, webmo )
Checking /home/webmo/webmo/users: Passed( 0777, webmo )
Checking /home/webmo/webmo/queue: Passed( 0777, webmo )
Checking /home/webmo/webmo/errors: Passed( 0777, webmo )

Checking Scratch Directory
Checking /tmp/webmo: Passed( 0777, webmo )

Checking Apache Configuration
Checking for AddHandler cgi-scripts enabled: Passed
Checking for UserDir enabled: Passed
Checking for suExec enabled: Disabled
No changes are necessary
Apache is running as user apache
Document root directory is /var/www/html
Script alias directory is /var/www/cgi-bin/ (URL: /cgi-bin/)

WebMO Configuration File
backgroundGraphic="background_dna.gif"
catPath="/bin/cat"
cgiBase="/home/webmo/public_html/cgi-bin/webmo"
cpPath="/bin/cp"
externalBatchQueue=""
host="omac110.chem.rug.nl"
htmlBase="/home/webmo/public_html/webmo"
killPath="/bin/kill"
license="####-####-####"
mkdirPath="/bin/mkdir"
mvPath="/bin/mv"
owner="Computational Chemistry on the WWW"
perlPath="/usr/bin/perl"
psOptions="-ef"
psPath="/bin/ps"
psRegExp="(\$pid, \$ppid, \$cpu_time) = /.{8}(.{6})(.{6}).{3}.{6}.{6}(.{12}).*/"
rcpPath="/usr/bin/rcp"
rmPath="/bin/rm"
rshPath="/usr/bin/rsh"
scpOptions="-o Protocol=1"
scpPath="/usr/bin/scp"
sendmailOptions="-t"
sendmailPath="/usr/sbin/sendmail"
servers="omac110.chem.rug.nl,0"
sshOptions="-o Protocol=1"
sshPath="/usr/bin/ssh"
systemScratch="/tmp"
tableBackgroundColor="#99cccc"
tarOptions="cf"
tarPath="/bin/tar"
unamePath="/bin/uname"
url_cgiBase="/~webmo/cgi-bin/webmo"
url_htmlBase="/~webmo/webmo"
userBase="/home/webmo/webmo"
version="6.0.001"
webserver="autodetect"
whereisPath="/usr/bin/whereis"
--

It complains about suexec being disabled, but when I enable it the script does not run at all and then the diagnose script gives no errors.
Hurenkamp
Posted on Friday, July 22, 2005 - 8:02 am:   

To add to this:

line 17 in login.cgi is: require("parse.cgi");

This file is present and the rights on this file are the same as for the other ones.
schmidt
Posted on Friday, July 22, 2005 - 1:08 pm:   

If you disabled suexec then you will need to reinstall WebMO, as the file permissions are not set up correctly (since it was ON, but now is OFF).

However, I recommend keeping suexec on. Check the suexec error log (in the /var/log/httpd directory) if you are having problems, and you should be able to resolve the errors.
Hurenkamp
Posted on Sunday, July 24, 2005 - 6:18 pm:   

In the end the problem was related to SELinux, incorporated into Red Hat 4 AS. Giving the following errors in var/log/messages :

Jul 24 22:26:03 ###### kernel: audit(1122236763.719:0): avc: denied { search } for pid=11052 comm=suexec name=webmo dev=dm-0 ino=14254083 scontext=root:system_r:httpd_suexec_t tcontext=root:object_r:user_home_dir_t tclass=dir

Disabling SELinux for apache (httpd) solved the problem for now. However it should be possible to set the properties for the files to allow suexec to access them.
schmidt
Posted on Sunday, July 31, 2005 - 2:03 pm:   

The following page documents how to set up Fedora Core 3 (and higher, probably) to run cgi-scripts and other content from user home directories WITHOUT disabling SELinux. It is slightly involved, but seems to be thorough.

http://fedora.redhat.com/docs/selinux-apache-fc3/sn-user-homedir.html
Kothanda Rama pichaandi
Unregistered guest
Posted on Thursday, June 21, 2007 - 8:53 pm:   

I am having problem with the z matrix editor.When I tried to fix the dihedral angle for a molecule and do the optimization,it changed the dihdral angle at the end of optimization.is there a way to solve this problem.I am trying to find the energies of rotational isomers
Anonymous
 
Posted on Wednesday, January 28, 2009 - 8:34 am:   

i had installed webmo on windows but its always giving failed status for every job.firstly it was not recognising the mopac path ,i m really puzzled ,plz help me out.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 71
Registered: 11-2006
Posted on Wednesday, January 28, 2009 - 9:06 am:   

First, make sure you have (separately) installed MOPAC for 'all windows'.

After doing so, log into WebMO as the use 'admin' and go to the 'Interface Manager' Enable 'Mopac' and click the 'Edit' button. Make sure to modify the path to MOPAC to match your installation directory, and hit 'Submit'. If there are no error messages, you should be set up to run MOPAC jobs from within WebMO.
shahinda
Unregistered guest
Posted on Saturday, January 31, 2009 - 8:09 am:   

i have done all d things as told by u but d problem still persists,
i had installed MOPAC2009 for all windows bt in the webmo interface manager in its iedit option its version is mentioned till 2007 only.
does d problem is becoz of this?
plz reply
JR Schmidt
Moderator
Username: Schmidt

Post Number: 72
Registered: 11-2006
Posted on Saturday, January 31, 2009 - 10:57 am:   

Yes. WebMO currently only supports MOPAC 2007. I will release and update that resolves this soon.

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