subject:"\[Rdkit\-discuss\] problem with RDKit configuration on apache and wsgi"

[Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Michał Nowotka

I have some problems with configuring apache to use rdkit,  this is
described in SO question:

http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library

Any help would be appreciated!

Regards,
Michał Nowotka
--
How ServiceNow helps IT people transform IT departments:
1. Consolidate legacy IT systems to a single system of record for IT
2. Standardize and globalize service processes across IT
3. Implement zero-touch automation to replace manual, redundant tasks
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Markus Sitzmann

Are you trying to use it with python/mod_wsgi? Your description so far is a bit vague :-)MarkusOn Tue, 10 Sep 2013 15:00:55 -0400, Michał Nowotka wrote:Thanks for advices. Unfortunately I can't do anything system-wide as I don't have administrator privileges on the server. Than also means I can't switch selinux.
On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov wrote:
Some kind of an answer seems to be already given at Stackoverflow.I would add two comments:1) Unless there are some specific problems with this you can add new library system-wide through ld.so.conf

2) You did not mention what your log files say but I would experiment with Selinux switched off.On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka wrote:

I have some problems with configuring apache to use rdkit, this is described in SO question:

http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library

Any help would be appreciated!Regards,Michał Nowotka
--
How ServiceNow helps IT people transform IT departments:
1. Consolidate legacy IT systems to a single system of record for IT
2. Standardize and globalize service processes across IT
3. Implement zero-touch automation to replace manual, redundant tasks
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2. Standardize and globalize service processes across IT
3. Implement zero-touch automation to replace manual, redundant tasks
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Michał Nowotka

Yes: python, mod_wsgi, vitualenv, RHEL


On Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann wrote:

> **
> Are you trying to use it with python/mod_wsgi? Your description so far is
> a bit vague :-)
>
> Markus
>
> On Tue, 10 Sep 2013 15:00:55 -0400, Michał Nowotka 
> wrote:
>
> Thanks for advices. Unfortunately I can't do anything system-wide as I
> don't have administrator privileges on the server. Than also means I can't
> switch selinux.
>
>
> On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov 
> wrote:
>
>> Some kind of an answer seems to be already given at Stackoverflow.
>> I would add two comments:
>> 1) Unless there are some specific problems with this you can add new
>> library system-wide through ld.so.conf
>> 2) You did not mention what your log files say but I would experiment
>> with Selinux switched off.
>>
>>
>>
>> On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka  wrote:
>>
>>> I have some problems with configuring apache to use rdkit,  this is
>>> described in SO question:
>>>
>>>
>>> http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library
>>>
>>> Any help would be appreciated!
>>>
>>> Regards,
>>> Michał Nowotka
>>>
>>>
>>> --
>>> How ServiceNow helps IT people transform IT departments:
>>> 1. Consolidate legacy IT systems to a single system of record for IT
>>> 2. Standardize and globalize service processes across IT
>>> 3. Implement zero-touch automation to replace manual, redundant tasks
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=5127&iu=/4140/ostg.clktrk
>>> ___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
>
>
>
>
--
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1. Consolidate legacy IT systems to a single system of record for IT
2. Standardize and globalize service processes across IT
3. Implement zero-touch automation to replace manual, redundant tasks
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Markus Sitzmann

So you mean, you have even RDKit running with this setup on other machinesor just the other libraries.If "other machines" vs the trouble maker machine includes a change from RH5 to RH6 than indeed I would suspect SELinux as Igor suggested. Don't ask mefor a solution except for switching it off.Is there anything (else) in /var/log/httpd/error_log?MarkusOn Tue, 10 Sep 2013 15:36:27 -0400, Michał Nowotka wrote:Yes, I can. What is more important I successfully managed to run other
libraries with extensions in C (indigo toolkit, cx_Oracle). What is even
more important the same configuration (at least it seems to be the
same) works on other machines. Unfortunately I don't know how to debug
to find source of my problemsOn Tue, Sep 10, 2013 at 9:32 PM, Markus Sitzmann wrote:

How far is your setup working so far? Can you already run python scriptsvia mod_wsgi without importing rdkit?
On Tue, 10 Sep 2013 15:29:07 -0400, Michał Nowotka wrote:
Yes: python, mod_wsgi, vitualenv, RHELOn Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann wrote:

Are you trying to use it with python/mod_wsgi? Your description so far is a bit vague :-)Markus
On Tue, 10 Sep 2013 15:00:55 -0400, Michał Nowotka wrote:

Thanks for advices. Unfortunately I can't do anything system-wide as I don't have administrator privileges on the server. Than also means I can't switch selinux.

On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov wrote:

Some kind of an answer seems to be already given at Stackoverflow.I would add two comments:1) Unless there are some specific problems with this you can add new library system-wide through ld.so.conf

2) You did not mention what your log files say but I would experiment with Selinux switched off.On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka wrote:

I have some problems with configuring apache to use rdkit, this is described in SO question:

http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library

Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Michał Nowotka

Yes, I mean even RDKit.

No, the trouble maker has exactly the same system. The only difference is
that in order to install my app on other machines I was using fabric and on
the problematic machines I just rsynced directories from working machines.

The only error in error_log is:

ImportError: libRDGeneral.so.1: cannot open shared object file: No
such file or directory




On Tue, Sep 10, 2013 at 9:47 PM, Markus Sitzmann wrote:

> **
> So you mean, you have even RDKit running with this setup on other machines
> or just the other libraries.
>
> If "other machines" vs the trouble maker machine includes a change from
> RH5
> to RH6 than indeed I would suspect SELinux as Igor suggested. Don't ask me
> for a solution except for switching it off.
>
> Is there anything (else) in /var/log/httpd/error_log?
>
> Markus
>
> On Tue, 10 Sep 2013 15:36:27 -0400, Michał Nowotka 
> wrote:
>
> Yes, I can. What is more important I successfully managed to run other
> libraries with extensions in C (indigo toolkit, cx_Oracle). What is even
> more important the same configuration (at least it seems to be the same)
> works on other machines. Unfortunately I don't know how to debug to find
> source of my problems
>
>
> On Tue, Sep 10, 2013 at 9:32 PM, Markus Sitzmann 
> wrote:
>
>> How far is your setup working so far? Can you already run python scripts
>> via mod_wsgi without importing rdkit?
>>
>>
>>
>>
>> On Tue, 10 Sep 2013 15:29:07 -0400, Michał Nowotka 
>> wrote:
>>
>> Yes: python, mod_wsgi, vitualenv, RHEL
>>
>>
>> On Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann 
>> wrote:
>>
>>> Are you trying to use it with python/mod_wsgi? Your description so far
>>> is a bit vague :-)
>>>
>>> Markus
>>>
>>> On Tue, 10 Sep 2013 15:00:55 -0400, Michał Nowotka 
>>> wrote:
>>>
>>> Thanks for advices. Unfortunately I can't do anything system-wide as I
>>> don't have administrator privileges on the server. Than also means I can't
>>> switch selinux.
>>>
>>>
>>> On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov <
>>> igor.v.filip...@gmail.com> wrote:
>>>
 Some kind of an answer seems to be already given at Stackoverflow.
 I would add two comments:
 1) Unless there are some specific problems with this you can add new
 library system-wide through ld.so.conf
 2) You did not mention what your log files say but I would experiment
 with Selinux switched off.



 On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka wrote:

> I have some problems with configuring apache to use rdkit,  this is
> described in SO question:
>
>
> http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library
>
> Any help would be appreciated!
>
> Regards,
> Michał Nowotka
>
>
> --
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
> 2. Standardize and globalize service processes across IT
> 3. Implement zero-touch automation to replace manual, redundant tasks
>
> http://pubads.g.doubleclick.net/gampad/clk?id=5127&iu=/4140/ostg.clktrk
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>

>>>
>>>
>>>
>>>
>>
>>
>>
>>
>
>
>
>
--
How ServiceNow helps IT people transform IT departments:
1. Consolidate legacy IT systems to a single system of record for IT
2. Standardize and globalize service processes across IT
3. Implement zero-touch automation to replace manual, redundant tasks
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Markus Sitzmann

How far is your setup working so far? Can you already run python scriptsvia mod_wsgi without importing rdkit? On Tue, 10 Sep 2013 15:29:07 -0400, Michał Nowotka wrote:Yes: python, mod_wsgi, vitualenv, RHELOn Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann wrote:

On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov wrote:

Some kind of an answer seems to be already given at Stackoverflow.I would add two comments:1) Unless there are some specific problems with this you can add new library system-wide through ld.so.conf

2) You did not mention what your log files say but I would experiment with Selinux switched off.On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka wrote:

I have some problems with configuring apache to use rdkit, this is described in SO question:

http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library

Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Michał Nowotka

Yes, I can. What is more important I successfully managed to run other
libraries with extensions in C (indigo toolkit, cx_Oracle). What is even
more important the same configuration (at least it seems to be the same)
works on other machines. Unfortunately I don't know how to debug to find
source of my problems


On Tue, Sep 10, 2013 at 9:32 PM, Markus Sitzmann wrote:

> **
> How far is your setup working so far? Can you already run python scripts
> via mod_wsgi without importing rdkit?
>
>
>
>
> On Tue, 10 Sep 2013 15:29:07 -0400, Michał Nowotka 
> wrote:
>
> Yes: python, mod_wsgi, vitualenv, RHEL
>
>
> On Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann 
> wrote:
>
>> Are you trying to use it with python/mod_wsgi? Your description so far is
>> a bit vague :-)
>>
>> Markus
>>
>> On Tue, 10 Sep 2013 15:00:55 -0400, Michał Nowotka 
>> wrote:
>>
>> Thanks for advices. Unfortunately I can't do anything system-wide as I
>> don't have administrator privileges on the server. Than also means I can't
>> switch selinux.
>>
>>
>> On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov > > wrote:
>>
>>> Some kind of an answer seems to be already given at Stackoverflow.
>>> I would add two comments:
>>> 1) Unless there are some specific problems with this you can add new
>>> library system-wide through ld.so.conf
>>> 2) You did not mention what your log files say but I would experiment
>>> with Selinux switched off.
>>>
>>>
>>>
>>> On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka wrote:
>>>
 I have some problems with configuring apache to use rdkit,  this is
 described in SO question:


 http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library

 Any help would be appreciated!

 Regards,
 Michał Nowotka


 --
 How ServiceNow helps IT people transform IT departments:
 1. Consolidate legacy IT systems to a single system of record for IT
 2. Standardize and globalize service processes across IT
 3. Implement zero-touch automation to replace manual, redundant tasks

 http://pubads.g.doubleclick.net/gampad/clk?id=5127&iu=/4140/ostg.clktrk
 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


>>>
>>
>>
>>
>>
>
>
>
>
--
How ServiceNow helps IT people transform IT departments:
1. Consolidate legacy IT systems to a single system of record for IT
2. Standardize and globalize service processes across IT
3. Implement zero-touch automation to replace manual, redundant tasks
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Michał Nowotka

Believe me, I restarted it many times :)


On Tue, Sep 10, 2013 at 10:06 PM, Igor Filippov
wrote:

> Maybe move the rdkit libs into some folder within apache DocumentRoot?
> Did you restart apache after syncing the libraries?
>
>
> On Tue, Sep 10, 2013 at 3:58 PM, Michał Nowotka  wrote:
>
>> Yes, I mean even RDKit.
>>
>> No, the trouble maker has exactly the same system. The only difference is
>> that in order to install my app on other machines I was using fabric and on
>> the problematic machines I just rsynced directories from working machines.
>>
>> The only error in error_log is:
>>
>> ImportError: libRDGeneral.so.1: cannot open shared object file: No such file 
>> or directory
>>
>>
>>
>>
>> On Tue, Sep 10, 2013 at 9:47 PM, Markus Sitzmann 
>> wrote:
>>
>>> **
>>> So you mean, you have even RDKit running with this setup on other
>>> machines
>>> or just the other libraries.
>>>
>>> If "other machines" vs the trouble maker machine includes a change from
>>> RH5
>>> to RH6 than indeed I would suspect SELinux as Igor suggested. Don't ask
>>> me
>>> for a solution except for switching it off.
>>>
>>> Is there anything (else) in /var/log/httpd/error_log?
>>>
>>> Markus
>>>
>>> On Tue, 10 Sep 2013 15:36:27 -0400, Michał Nowotka 
>>> wrote:
>>>
>>> Yes, I can. What is more important I successfully managed to run other
>>> libraries with extensions in C (indigo toolkit, cx_Oracle). What is even
>>> more important the same configuration (at least it seems to be the same)
>>> works on other machines. Unfortunately I don't know how to debug to find
>>> source of my problems
>>>
>>>
>>> On Tue, Sep 10, 2013 at 9:32 PM, Markus Sitzmann >> > wrote:
>>>
 How far is your setup working so far? Can you already run python scripts
 via mod_wsgi without importing rdkit?




 On Tue, 10 Sep 2013 15:29:07 -0400, Michał Nowotka 
 wrote:

 Yes: python, mod_wsgi, vitualenv, RHEL


 On Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann <
 sitzm...@helix.nih.gov> wrote:

> Are you trying to use it with python/mod_wsgi? Your description so far
> is a bit vague :-)
>
> Markus
>
> On Tue, 10 Sep 2013 15:00:55 -0400, Michał Nowotka 
> wrote:
>
> Thanks for advices. Unfortunately I can't do anything system-wide as I
> don't have administrator privileges on the server. Than also means I can't
> switch selinux.
>
>
> On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov <
> igor.v.filip...@gmail.com> wrote:
>
>> Some kind of an answer seems to be already given at Stackoverflow.
>> I would add two comments:
>> 1) Unless there are some specific problems with this you can add new
>> library system-wide through ld.so.conf
>> 2) You did not mention what your log files say but I would experiment
>> with Selinux switched off.
>>
>>
>>
>> On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka wrote:
>>
>>> I have some problems with configuring apache to use rdkit,  this is
>>> described in SO question:
>>>
>>>
>>> http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library
>>>
>>> Any help would be appreciated!
>>>
>>> Regards,
>>> Michał Nowotka
>>>
>>>
>>> --
>>> How ServiceNow helps IT people transform IT departments:
>>> 1. Consolidate legacy IT systems to a single system of record for IT
>>> 2. Standardize and globalize service processes across IT
>>> 3. Implement zero-touch automation to replace manual, redundant tasks
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=5127&iu=/4140/ostg.clktrk
>>> ___
>>> Rdkit-discuss mailing list
>>> Rdkit-discuss@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>
>
>
>
>




>>>
>>>
>>>
>>>
>>
>>
>> --
>> How ServiceNow helps IT people transform IT departments:
>> 1. Consolidate legacy IT systems to a single system of record for IT
>> 2. Standardize and globalize service processes across IT
>> 3. Implement zero-touch automation to replace manual, redundant tasks
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=5127&iu=/4140/ostg.clktrk
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
--
How ServiceNow helps IT people transform IT departments:
1. Consolidate legacy IT systems to a single system of record for IT
2. Standardize and globalize service processes across IT
3. Implement zero-touch automati

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Michał Nowotka

Thanks for advices. Unfortunately I can't do anything system-wide as I
don't have administrator privileges on the server. Than also means I can't
switch selinux.


On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov wrote:

> Some kind of an answer seems to be already given at Stackoverflow.
> I would add two comments:
> 1) Unless there are some specific problems with this you can add new
> library system-wide through ld.so.conf
> 2) You did not mention what your log files say but I would experiment with
> Selinux switched off.
>
>
>
> On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka  wrote:
>
>> I have some problems with configuring apache to use rdkit,  this is
>> described in SO question:
>>
>>
>> http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library
>>
>> Any help would be appreciated!
>>
>> Regards,
>> Michał Nowotka
>>
>>
>> --
>> How ServiceNow helps IT people transform IT departments:
>> 1. Consolidate legacy IT systems to a single system of record for IT
>> 2. Standardize and globalize service processes across IT
>> 3. Implement zero-touch automation to replace manual, redundant tasks
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=5127&iu=/4140/ostg.clktrk
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
--
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1. Consolidate legacy IT systems to a single system of record for IT
2. Standardize and globalize service processes across IT
3. Implement zero-touch automation to replace manual, redundant tasks
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Igor Filippov

Maybe move the rdkit libs into some folder within apache DocumentRoot?
Did you restart apache after syncing the libraries?


On Tue, Sep 10, 2013 at 3:58 PM, Michał Nowotka  wrote:

> Yes, I mean even RDKit.
>
> No, the trouble maker has exactly the same system. The only difference is
> that in order to install my app on other machines I was using fabric and on
> the problematic machines I just rsynced directories from working machines.
>
> The only error in error_log is:
>
> ImportError: libRDGeneral.so.1: cannot open shared object file: No such file 
> or directory
>
>
>
>
> On Tue, Sep 10, 2013 at 9:47 PM, Markus Sitzmann 
> wrote:
>
>> **
>> So you mean, you have even RDKit running with this setup on other machines
>> or just the other libraries.
>>
>> If "other machines" vs the trouble maker machine includes a change from
>> RH5
>> to RH6 than indeed I would suspect SELinux as Igor suggested. Don't ask me
>> for a solution except for switching it off.
>>
>> Is there anything (else) in /var/log/httpd/error_log?
>>
>> Markus
>>
>> On Tue, 10 Sep 2013 15:36:27 -0400, Michał Nowotka 
>> wrote:
>>
>> Yes, I can. What is more important I successfully managed to run other
>> libraries with extensions in C (indigo toolkit, cx_Oracle). What is even
>> more important the same configuration (at least it seems to be the same)
>> works on other machines. Unfortunately I don't know how to debug to find
>> source of my problems
>>
>>
>> On Tue, Sep 10, 2013 at 9:32 PM, Markus Sitzmann 
>> wrote:
>>
>>> How far is your setup working so far? Can you already run python scripts
>>> via mod_wsgi without importing rdkit?
>>>
>>>
>>>
>>>
>>> On Tue, 10 Sep 2013 15:29:07 -0400, Michał Nowotka 
>>> wrote:
>>>
>>> Yes: python, mod_wsgi, vitualenv, RHEL
>>>
>>>
>>> On Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann >> > wrote:
>>>
 Are you trying to use it with python/mod_wsgi? Your description so far
 is a bit vague :-)

 Markus

 On Tue, 10 Sep 2013 15:00:55 -0400, Michał Nowotka 
 wrote:

 Thanks for advices. Unfortunately I can't do anything system-wide as I
 don't have administrator privileges on the server. Than also means I can't
 switch selinux.


 On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov <
 igor.v.filip...@gmail.com> wrote:

> Some kind of an answer seems to be already given at Stackoverflow.
> I would add two comments:
> 1) Unless there are some specific problems with this you can add new
> library system-wide through ld.so.conf
> 2) You did not mention what your log files say but I would experiment
> with Selinux switched off.
>
>
>
> On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka wrote:
>
>> I have some problems with configuring apache to use rdkit,  this is
>> described in SO question:
>>
>>
>> http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library
>>
>> Any help would be appreciated!
>>
>> Regards,
>> Michał Nowotka
>>
>>
>> --
>> How ServiceNow helps IT people transform IT departments:
>> 1. Consolidate legacy IT systems to a single system of record for IT
>> 2. Standardize and globalize service processes across IT
>> 3. Implement zero-touch automation to replace manual, redundant tasks
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=5127&iu=/4140/ostg.clktrk
>> ___
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>




>>>
>>>
>>>
>>>
>>
>>
>>
>>
>
>
> --
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Igor Filippov

Some kind of an answer seems to be already given at Stackoverflow.
I would add two comments:
1) Unless there are some specific problems with this you can add new
library system-wide through ld.so.conf
2) You did not mention what your log files say but I would experiment with
Selinux switched off.



On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka  wrote:

> I have some problems with configuring apache to use rdkit,  this is
> described in SO question:
>
>
> http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library
>
> Any help would be appreciated!
>
> Regards,
> Michał Nowotka
>
>
> --
> How ServiceNow helps IT people transform IT departments:
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-10 Thread Markus Sitzmann


What happens if you import RDKit into a regular python shell without mod_wsgion this computer? If this works than the mod_wsgi python maybe runs on another python interpreter.On Tue, 10 Sep 2013 16:08:24 -0400, Michał Nowotka  wrote:Believe me, I restarted it many times :)On Tue, Sep 10, 2013 at 10:06 PM, Igor Filippov  wrote:
Maybe move the rdkit libs into some folder within apache DocumentRoot?Did you restart apache after syncing the libraries?
On Tue, Sep 10, 2013 at 3:58 PM, Michał Nowotka  wrote:

Yes, I mean even RDKit.No, the trouble maker has exactly the same system. The only difference is that in order to install my app on other machines I was using fabric and on the problematic machines I just rsynced directories from working machines.


The only error in error_log is:ImportError: libRDGeneral.so.1: cannot open shared object file: No such file or directory


On Tue, Sep 10, 2013 at 9:47 PM, Markus Sitzmann  wrote:





So you mean, you have even RDKit running with this setup on other machinesor just the other libraries.If "other machines" vs the trouble maker machine includes a change from RH5 


to RH6 than indeed I would suspect SELinux as Igor suggested. Don't ask mefor a solution except for switching it off.Is there anything (else) in /var/log/httpd/error_log?


MarkusOn Tue, 10 Sep 2013 15:36:27 -0400, Michał Nowotka  wrote:


Yes, I can. What is more important I successfully managed to run other 
libraries with extensions in C (indigo toolkit, cx_Oracle). What is even
 more important the same configuration (at least it seems to be the 
same) works on other machines. Unfortunately I don't know how to debug 
to find source of my problemsOn Tue, Sep 10, 2013 at 9:32 PM, Markus Sitzmann  wrote:






How far is your setup working so far? Can you already run python scriptsvia mod_wsgi without importing rdkit? 
On Tue, 10 Sep 2013 15:29:07 -0400, Michał Nowotka  wrote:



Yes: python, mod_wsgi, vitualenv, RHELOn Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann  wrote:







Are you trying to use it with python/mod_wsgi? Your description so far is a bit vague :-)Markus
On Tue, 10 Sep 2013 15:00:55 -0400, Michał Nowotka  wrote:




Thanks for advices. Unfortunately I can't do anything system-wide as I don't have administrator privileges on the server. Than also means I can't switch selinux. 





On Tue, Sep 10, 2013 at 7:59 PM, Igor Filippov  wrote:





Some kind of an answer seems to be already given at Stackoverflow.I would add two comments:1) Unless there are some specific problems with this you can add new library system-wide through ld.so.conf






2) You did not mention what your log files say but I would experiment with Selinux switched off.On Tue, Sep 10, 2013 at 1:51 PM, Michał Nowotka  wrote:






I have some problems with configuring apache to use rdkit,  this is described in SO question:






http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library







Any help would be appreciated!Regards,Michał Nowotka
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-11 Thread Michał Nowotka

Hi Greg,

Problem solved! http://stackoverflow.com/a/18731255/940208
Maybe setting LD_RUN_PATH before compiling it's worth a paragraph in rdkit
docs?

Cheers,
Michał


On Wed, Sep 11, 2013 at 11:15 PM, greg landrum wrote:

> Hi Michal,
>
> This is, unfortunately, not easy.
>
> One solution to this (the one we use) is to modify the environment in the
> script that invokes apache and set LD_LIBRARY_PATH there..
>
> Another easy one is to install the rdkit shared libraries into a directory
> which is in the apache user's LD_LIBRARY_PATH, maybe /user/local/lib?
>
> If you can't convince your sys admins to do either of these for you, then
> you will have to figure out how to use the RPATH support that cmake has:
> http://www.cmake.org/Wiki/CMake_RPATH_handling
>
> I am away from my computer until next week, so, I can't offer any real,
> help aside from pointing at that page.
>
> Once I am back I will definitely spend some time on this to see if it is
> possible to simplify the process.
>
> -greg
>
>
> On Sep 11, 2013, at 2:51 AM, Michał Nowotka  wrote:
>
> I have some problems with configuring apache to use rdkit,  this is
> described in SO question:
>
>
> http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library
>
> Any help would be appreciated!
>
> Regards,
> Michał Nowotka
>
>
> --
>
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
> 2. Standardize and globalize service processes across IT
> 3. Implement zero-touch automation to replace manual, redundant tasks
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>
> ___
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>
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-11 Thread greg landrum

Hi Michal,

This is, unfortunately, not easy.

One solution to this (the one we use) is to modify the environment in the 
script that invokes apache and set LD_LIBRARY_PATH there.. 

Another easy one is to install the rdkit shared libraries into a directory 
which is in the apache user's LD_LIBRARY_PATH, maybe /user/local/lib?

If you can't convince your sys admins to do either of these for you, then you 
will have to figure out how to use the RPATH support that cmake has:
http://www.cmake.org/Wiki/CMake_RPATH_handling

I am away from my computer until next week, so, I can't offer any real, help 
aside from pointing at that page.

Once I am back I will definitely spend some time on this to see if it is 
possible to simplify the process.

-greg


On Sep 11, 2013, at 2:51 AM, Michał Nowotka  wrote:

> I have some problems with configuring apache to use rdkit,  this is described 
> in SO question:
> 
> http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library
> 
> Any help would be appreciated!
> 
> Regards,
> Michał Nowotka
> --
> How ServiceNow helps IT people transform IT departments:
> 1. Consolidate legacy IT systems to a single system of record for IT
> 2. Standardize and globalize service processes across IT
> 3. Implement zero-touch automation to replace manual, redundant tasks
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> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-11 Thread Greg Landrum

Glad the problem is solved. Thanks for the link. Including something like
this in the docs would be a good idea.

-greg

On Thursday, September 12, 2013, Michał Nowotka wrote:

> Hi Greg,
>
> Problem solved! http://stackoverflow.com/a/18731255/940208
> Maybe setting LD_RUN_PATH before compiling it's worth a paragraph in rdkit
> docs?
>
> Cheers,
> Michał
>
>
> On Wed, Sep 11, 2013 at 11:15 PM, greg landrum 
> 
> > wrote:
>
>> Hi Michal,
>>
>> This is, unfortunately, not easy.
>>
>> One solution to this (the one we use) is to modify the environment in the
>> script that invokes apache and set LD_LIBRARY_PATH there..
>>
>> Another easy one is to install the rdkit shared libraries into a
>> directory which is in the apache user's LD_LIBRARY_PATH, maybe
>> /user/local/lib?
>>
>> If you can't convince your sys admins to do either of these for you, then
>> you will have to figure out how to use the RPATH support that cmake has:
>> http://www.cmake.org/Wiki/CMake_RPATH_handling
>>
>> I am away from my computer until next week, so, I can't offer any real,
>> help aside from pointing at that page.
>>
>> Once I am back I will definitely spend some time on this to see if it is
>> possible to simplify the process.
>>
>> -greg
>>
>>
>> On Sep 11, 2013, at 2:51 AM, Michał Nowotka 
>> >
>> wrote:
>>
>> I have some problems with configuring apache to use rdkit,  this is
>> described in SO question:
>>
>>
>> http://stackoverflow.com/questions/2550504/setting-ld-library-path-in-apache-passenv-setenv-still-cant-find-library
>>
>> Any help would be appreciated!
>>
>> Regards,
>> Michał Nowotka
>>
>>
>> --
>>
>> How ServiceNow helps IT people transform IT departments:
>> 1. Consolidate legacy IT systems to a single system of record for IT
>> 2. Standardize and globalize service processes across IT
>> 3. Implement zero-touch automation to replace manual, redundant tasks
>>
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>>
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>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-11 Thread Gianluca Sforna

On Thu, Sep 12, 2013 at 12:25 AM, Greg Landrum  wrote:
> Glad the problem is solved.

And without disabling SELinux :)

http://stopdisablingselinux.com/


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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-11 Thread Markus Sitzmann


> And without disabling SELinux :)
>
> http://stopdisablingselinux.com/

I never said that is a good idea :-)

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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-11 Thread Markus Sitzmann

Although, since the NSA was involved into the development of SELinux
maybe it doesn't matter so much anymore :-)


On Wed, 11 Sep 2013 18:42:20 -0400, Markus Sitzmann  
 wrote:

>
>> And without disabling SELinux :)
>>
>> http://stopdisablingselinux.com/
>
> I never said that is a good idea :-)
>
> --
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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

2013-09-12 Thread Gianluca Sforna

On Thu, Sep 12, 2013 at 1:01 AM, Markus Sitzmann  wrote:
> Although, since the NSA was involved into the development of SELinux
> maybe it doesn't matter so much anymore :-)

It's not that I audited the code myself but... even if originated fron
NSA, it is a piece of open source software, so I tend to trust it more
than many other things like, hard disks
http://spritesmods.com/?art=hddhack
:)



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[Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

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Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi

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