Re: [Rdkit-discuss] problem with RDKit configuration on apache and wsgi
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 mmm...@gmail.com 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 mmm...@gmail.com 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=5127iu=/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=5127iu=/4140/ostg.clktrk___ 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
Yes: python, mod_wsgi, vitualenv, RHEL On Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann sitzm...@helix.nih.govwrote: ** 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 mmm...@gmail.com 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.comwrote: 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 mmm...@gmail.com 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=5127iu=/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=5127iu=/4140/ostg.clktrk___ 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
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 mmm...@gmail.com wrote:Yes: python, mod_wsgi, vitualenv, RHELOn 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 mmm...@gmail.com 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 mmm...@gmail.com 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=5127iu=/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=5127iu=/4140/ostg.clktrk___ 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
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 sitzm...@helix.nih.govwrote: ** 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 mmm...@gmail.com wrote: Yes: python, mod_wsgi, vitualenv, RHEL On Tue, Sep 10, 2013 at 9:22 PM, Markus Sitzmann sitzm...@helix.nih.govwrote: 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 mmm...@gmail.com 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 mmm...@gmail.comwrote: 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=5127iu=/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=5127iu=/4140/ostg.clktrk___ 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
Believe me, I restarted it many times :) On Tue, Sep 10, 2013 at 10:06 PM, Igor Filippov igor.v.filip...@gmail.comwrote: 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 mmm...@gmail.com 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 sitzm...@helix.nih.govwrote: ** 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 mmm...@gmail.com 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 sitzm...@helix.nih.gov 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 mmm...@gmail.com 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 mmm...@gmail.com 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 mmm...@gmail.comwrote: 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=5127iu=/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=5127iu=/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=5127iu=/4140/ostg.clktrk___ 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
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.comwrote: 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 mmm...@gmail.com 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=5127iu=/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=5127iu=/4140/ostg.clktrk___ 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
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 mmm...@gmail.com 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 sitzm...@helix.nih.govwrote: ** 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 mmm...@gmail.com 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 sitzm...@helix.nih.govwrote: 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 mmm...@gmail.com 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 mmm...@gmail.com 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 mmm...@gmail.comwrote: 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=5127iu=/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=5127iu=/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=5127iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
