Installation about molcalc HOT 12 CLOSED

Since "About" is getting a 404, I suspect the "rewrite" module is not turned on. It should be checked by the health_check.php, but can you double check that for me?
If you use Chrome then you can open the "Developer toolbar" (F12) to see in the console why the "calculate property" is stuck, but I'm guessing it is the same problem as "about".

regarding folders; no, it should not be the same,

• the datafolder (tmpfolder in settings) is where to store the log files for the molcalc (should be in the molcalc folder)
• the "scr" folder is where to put tempoary GAMESS files used for the calculation (if used locally, use the /tmp folder)

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You are right, although the module rewrite is enabled, the reason why GAMESS does not start is due to the 404 error. Chrome console shows: POST http://xxx.xx.x.xxx/initialize/initialize 404 (Not Found)
Might the reason be in the address? I have only an IP address.
Herewith, http://xxx.xx.x.xxx/views/pages/about.php opens. Also, editor.php, but not calculation.php.

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No, you should be able to open molcalc fine with a IP address. I would focus on getting the "about" page to load up, as I still think the problem is somehow the rewrite module in apache is not turned on.
Do you have "AllowOverride All" for the molcalc directory in the apache setup?
I would also recommend looking at "phpinfo();" to see if it is disabled.
https://stackoverflow.com/questions/3772892/phpinfo-mod-rewrite

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You are right. I have to change setting in /etc/apache2/ from "AllowOverride None" to "AllowOverride All". Then executing "service apache2 restart". I believe this could be added to the README.
The about page works.
Something is still wrong with gamess. Inputs are not copied to the scr folder. In the README, there is a mention of rungms_molcalc. Should I change the owner of privileges of the scr folder of something like that?

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rungms will probably not work by default, as www-user does not have a $HOME. You need to change the rungms to exclude that. If you are using /tmp as scr folder, then www-data should have privileges to use it.

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The input file in /data/XXX have permission "-rw-r--r--" (644). Is it right?
The resulting log-file looks like that:
"""
...
GAMESS temporary binary files will be written to /tmp
GAMESS supplementary output files will be written to /tmp
Copying input file 1bf7caa230106a3bd0689cc7be466332.inp to your run's scratch directory...
"""
When I change the privileges and run gamess manually, the calculation runs normally leading to a much longer log.
I have tried various combinations of privileges and ownerships without success. For the benefit of all potential users, could you please explain the logic behind the privileges? Is it so that www-data has the rights to write to data, it executes gamess in /tmp and writes the log to data/XXX?

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Yeah, I probably need to update the installation guide a bit.

Regarding data/*, yes, the user www-data needs to have write access to save log files (www-data is the apache web user).

Regarding rungms, which is the GAMESS executable, it is written a bit overly complicated and you need to hack it so it does not use environmental variables unavailable to www-data (i.e. the $HOME variable). This is why it works with your user. To test it properly you can sudo su www-data and try to to run GAMESS.

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After resolving all problems, I would be happy to commit updates to the README.
Two modifications allowed moving one step forward.
First, I have commented, although there is no .gmsrc:

#if (-e $HOME/.gmsrc) then
#   echo "reading your own $HOME/.gmsrc"
#   source $HOME/.gmsrc
#endif

Second, due to problems wtih /tmp, I decided to use "scr" folder with 777 permissions, like the "data".

set SCR=/home/user/gamess/scr
set USERSCR=/home/user/gamess/scr
#set SCR=/var
#set USERSCR=/var

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The next problem is that "calculation" show nothing. Neither /calculation nor /calculation/hash.
The html code is broken, it ends as

<!-- Content -->
<article>
<section class="container">

The data/hash folder contains necessary files, for example:
-rw-r--r-- 1 www-data www-data 471 Mar 11 00:24 8abc4396b8302086cb7ffef6413b2eac.inp
-rw-r--r-- 1 www-data www-data 62290 Mar 11 00:24 8abc4396b8302086cb7ffef6413b2eac.log
-rw-r--r-- 1 www-data www-data 349 Mar 11 00:24 coordinates_jmol.xyz
-rw-r--r-- 1 www-data www-data 599 Mar 11 00:24 coordinates.mol2
-rw-r--r-- 1 www-data www-data 308 Mar 11 00:24 coordinates.xyz
-rw-r--r-- 1 www-data www-data 76 Mar 11 00:24 molecule.db
-rw-r--r-- 1 www-data www-data 2195 Mar 11 00:24 thumbnail.png

Do you have ideas, what could be the reason?

UPDATE: there is if–else in the calculation.php. When the first condition is removed, the php-scripts shows the list of molecules.

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The error is located somewhere in between these lines:

<?php
    foreach($calculationTypes as $calculationType => $calculationName):
    $exists = is_dir($calculationType);
?>

    <div class="calculationtype <?php print $calculationType ?>">

        <?php if($exists): ?>

            <?php
                chdir($calculationType);
                require(CALPATH.'/'.$calculationType.'/view.php');
                chdir('..');
            ?>

        <?php else: ?>

            <p><a class="button calculate-now">Calculate</a></p>

        <?php endif; ?>


        <div class="clean"></div>
    </div>

<?
    endforeach;
?>

Apache log hints to "PHP Parse error: syntax error, unexpected 'else' (T_ELSE) in /var/www/molcalc/views/pages/calculation.php on line 119". This line is "".
Could you please check if calculation.php is the same on your working server molcalc.org?

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Hurray! There is an error.
Should be

<?php
    endforeach;
?>

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Ah, right, the php parser moved away from <? ?> being usable in code. for some reason.
Is everything working now then?

I will accept the pull requests.

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