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August 24, 2019

WebMO -- Troubles getting Gaussian Ru... Log Out | Topics | Search
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Adam Lesser
Unregistered guest
Posted on Sunday, August 24, 2008 - 3:37 am:   

prelude: I have read in detail the https://www.webmo.net/support/binaries_linux.html#gaussian page.. and am having major troubles with installing gaussian for use with webmo. My current setup which works fine for users executing gaussian via the command line is as follows:

Gaussian directory is at /opt/gaussian/g03/ (the g03 executable full path would therefore be /opt/gaussian/g03/g03)

I configured WebMO with this information but then I tried to run a standard gaussian job and as output got :

"Cannot execute /opt/gaussian/g03/g03: Permission denied"

I figured out that my apache2 setup uses the "www-data" user to run the job (at least it does for MOPAC2007, which works perfectly fine) and so I added www-data to my "users" group via "usermod -a -G users www-data" since the permissions on the gaussian folder have "users" set as the group. Unfortunately this did not work at all as far as I can tell and I still get the same error.

When I "sudo su www-data" from my terminal and try to run g03 I get a different error:

www-data@wmm:/opt/gaussian/g03$ ./g03
Entering Gaussian System, Link 0=./g03
PGFIO/stdio: Permission denied
PGFIO-F-/OPEN/unit=11/error code returned by host stdio - 13.
File name = /opt/gaussian/g03/Gau-8693.inp
In source file ml0.f, at line number 179


I've tried making the gaussian folder world executable (i.e. chmod -R 755) but I quickly found that that lead to gaussian complaining:

Entering Gaussian System, Link 0=/opt/gaussian/g03/g03
Files in the Gaussian directory are world accessible.
This must be fixed


Ideas/solutions would be greatly appreciated.

I'm running the desktop distribution of Ubuntu 8.10 by the way (so people understand how i'm setup).
JR Schmidt
Moderator
Username: Schmidt

Post Number: 46
Registered: 11-2006
Posted on Sunday, August 24, 2008 - 10:21 am:   

The best way to accomplish what you want is use 'suexec' to run WebMO under a normal username.

To do this, create a 'webmo' account (or user an existing user account) and install WebMO into the /home/username/public_html directory sttructure, as suggested during installation.

It may also be necessary to enable suexec, by doing a chmod 4755 /usr/sbin/suexec.

This should make the WebMO application run under user 'username'. Adding that user to the 'gaussian' group should solve the problem.
Adam Lesser
Unregistered guest
Posted on Sunday, August 24, 2008 - 2:02 pm:   

Since the only purpose of the webserver on the machine was to serve webmo I installed it to it's document root @ /var/www, but I guess this seems like a better option.
Anonymous
 
Posted on Tuesday, March 02, 2010 - 3:36 am:   

I am using ovgf=full option with g03 to get the IP of clusters. The log file lists the pole strenghs of high lying alpha and beta spin orbitals( actual and virtual both). Can the value corersponding to HOMO be taken as the IP of the cluster as a whole
?
Brian Moore
Unregistered guest
Posted on Tuesday, March 23, 2010 - 11:58 am:   

I just installed the free version of WebMO and just ran a successful g09 job after first seeing the same error mentioned here--
Cannot execute /usr/local/g09/g09: Permission denied

Now, in my case I DID install webmo under an existing user account and put WebMO into /home/[user]/public_html as mentioned above.

However, since it was not running, what I tried was this--I looked at the list of users, noticed a user wwwrun. I added wwwrun to the gaussian group and also put the startup script into wwwrun's .bashrc file.

As per the Gaussian install instructions, these lines in .bashrc look like:

g09root="/usr/local"
GAUSS_SCRDIR="/tmp"
export g09root GAUSS_SCRDIR
. $g09root/g09/bsd/g09.profile

Now it seems to be working OK so far.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 148
Registered: 11-2006
Posted on Tuesday, March 23, 2010 - 12:07 pm:   

In most cases installing WebMO under a user home directory will be sufficient -- in most system configuration, this makes WebMO run under the UID of that user. But not always!

In the above case, WebMO was running under the UID of 'wwwrun', which then needed to be added to the 'gaussian' group for permission to run g09.
Anonymous
 
Posted on Wednesday, September 29, 2010 - 5:16 pm:   

I want to install the WebMo server in my local machine to run locally. Wish server name should i give during the installation?
My machine name "almeida-desktop" and i'm out of my work network domain.
I tried with "localhost" and my ip number. Other times Apache server don't find the URL of login.

Any hints...?? Thanks
JR Schmidt
Moderator
Username: Schmidt

Post Number: 163
Registered: 11-2006
Posted on Wednesday, September 29, 2010 - 5:24 pm:   

Since you are using it on your local machine, I would use "localhost". You should then access your machine with the URL http://localhost/cgi-bin/webmo/login.cgi

This will work fine so long as you access the installation FROM your computer, which is probably what you want to do anyway.

Assume your (Windows?) machine is properly configured, this should work fine. Most likely the problem with "almeida-desktop" is that it contains a dash.
Anonymous
 
Posted on Monday, March 14, 2011 - 9:23 am:   

How to calculate absorption and fluorescence characteristics using gaussian 03 package?plz give details...
Anonymous
 
Posted on Friday, September 30, 2011 - 7:32 am:   

tried to install webMo on Ubuntu 10.04 as explained in your tutorial using default directories....but unbale to access webMo form a browser. it give following error message... how can i configure this installation as virtual host and access it through browser?. (apache2 is configured and default page is accessible)
======================
Error message,

Not Found

The requested URL /~web/cgi-bin/webmo/login.cgi was not found on this server.
Apache/2.2.14 (Ubuntu) Server at 192.168.1.125 Port 80
Anonymous
 
Posted on Friday, September 30, 2011 - 7:57 am:   

Can any body tell me the exact document root to set up webMO on an Ubuntu 10.04 server? and which will enable us to access webMO through browsers on LAN pc's?. Provided installed with default directories as explained in webMO tutorial. Kindly check with an Ubuntu 10.04 system and respond back with details
<virtualhost>
ServerName ?
DocumentRoot /path/to/your/project/root ?
<directory> ?
AllowOverride All
Order deny,allow
Allow from all
</directory>
</virtualhost>
Anonymous
 
Posted on Tuesday, November 06, 2012 - 9:39 am:   

Hello!
I made the terrible mistake of upgrading my server OpenSuse 64 bit and webmo went off the cyberspace..
Gaussian went off. not everything.
However. I am not able to find suexec at all
there is something called suexec2 and I decided to
chmod 4755 /usr/sbin/suexec.
making that "4755" and it did not seem to help.
I tried upgrading it to webmo 13 and then reinstalling webmo. IT did not help !!
Cannot execute /usr/local/bin/g09/g09: Permission denied
This is the only reply I get..
JR Schmidt
Moderator
Username: Schmidt

Post Number: 318
Registered: 11-2006
Posted on Tuesday, November 06, 2012 - 10:01 am:   

suexec2 is the replacement for suexec. It should be what you want. The fact that you get a permission denied suggests that suexec is not actually being used.
Carrie Miller
Unregistered guest
Posted on Wednesday, May 22, 2013 - 7:46 pm:   

I am having the same error (permission denied) when trying to run g09 through webmo on Mac OS 10.8.3. Gaussian runs fine through the command line.

I installed webmo in the local user account, as suggested by the install directions. (I followed all the instructions on https://www.webmo.net/support/installation_osx.html)

I do not have anything called /etc/sbin/suexec or suexec2 (I'm not sure if this is a linux vs mac issue).
JR Schmidt
Moderator
Username: Schmidt

Post Number: 353
Registered: 11-2006
Posted on Thursday, May 23, 2013 - 10:13 am:   

suexec is not included in OS X anymore. It CAN be installed, but it is a bit of a pain. As such, the easiest solution is probably to add the user '_www' to the 'gaussian' group.

This is because the WegbMO scripts run under the user ID of '_www' since they are run by the Apache web server. Gaussian is only allowed to be run by users in the 'gaussian' group (or whatever group name you decided when installing Gaussian).

Alternatively, if you ONLY run Gaussian via WebMO, you can change the group owner of the g09 binary to '_www'.
Tim
Unregistered guest
Posted on Saturday, February 10, 2018 - 11:40 pm:   

Gaussian can't run the test in Terminal- says it can't find the test001.com file, even though it's right there in the g09 folder! WebMO also cannot run Gaussian.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 600
Registered: 11-2006
Posted on Sunday, February 11, 2018 - 10:15 pm:   

Please read the Gaussian installation instructions:

https://www.webmo.net/support/binaries_linux.html#gaussian

There are specific steps for how to run jobs, etc.
Patrick E. Fleming
Unregistered guest
Posted on Thursday, July 18, 2019 - 6:37 pm:   

I have run into the issue a few times. I am currently running Ubuntu 19.04 on a Ryzen3 2200G build. My set up has $g16root = /usr/local/bin, webmo (Version 19.0) is its own user and has been added the the "gaussian" group. g16 runs fine from the command line. However, I was still getting the "Permission denied" error when attempting to run a gaussian job through WebMO.

my current solution was to

cd $g16root
sudo chown -R www-data:gaussian g16

Then all worked fine.
JR Schmidt
Moderator
Username: Schmidt

Post Number: 644
Registered: 11-2006
Posted on Friday, July 19, 2019 - 1:11 pm:   

Your solution is fine. The reason that your first solution (simply adding the 'webmo' user to the 'gaussian group) didn't work is that 'suexec' is not enabled by default on Unbuntu. This means that the WebMO scripts (and resulting jobs) are running as user 'www-data' rather than 'webmo'.

If you want to enable suexec at this point (which will require reinstalling WebMO, and/or fixing lots of permissions), you can do so by following the following instructions:

https://www.webmo.net/link/help/ConfiguringApache.html

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