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Install PyRODS @uppmax #19

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brainstorm opened this Issue Apr 18, 2012 · 10 comments

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@jhagberg jhagberg was assigned Apr 18, 2012

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jhagberg commented Apr 20, 2012

Is this the same for iRODS 3.1?

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brainstorm commented Apr 20, 2012

It's a general gcc compiler flag, it should. Just try it ;)

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jhagberg commented Apr 20, 2012

I have now recompiled u5

in
config/irods.config

change setting to
$CCFLAGS = '-fPIC';

Please have a try!

@jhagberg jhagberg closed this Apr 20, 2012

@brainstorm brainstorm reopened this Apr 20, 2012

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brainstorm commented Apr 20, 2012

No dice :-/

(py2.7)[roman@u5 PyRods-3.1.0 0]$ python setup.py build
(...)
g++ -shared build/temp.linux-x86_64-2.6/./src/irods.o build/temp.linux-x86_64-2.6/./src/PyApiNumber.o build/temp.linux-x86_64-2.6/./src/PyAuth.o build/temp.linux-x86_64-2.6/./src/PyChkObjPermAndStat.o build/temp.linux-x86_64-2.6/./src/PyDataObj.o build/temp.linux-x86_64-2.6/./src/PyGetRodsEnv.o build/temp.linux-x86_64-2.6/./src/PyMd5.o build/temp.linux-x86_64-2.6/./src/PyMiscUtil.o build/temp.linux-x86_64-2.6/./src/PyModAccessControl.o build/temp.linux-x86_64-2.6/./src/PyMsParam.o build/temp.linux-x86_64-2.6/./src/PyObf.o build/temp.linux-x86_64-2.6/./src/PyParseCommandLine.o build/temp.linux-x86_64-2.6/./src/PyRcConnect.o build/temp.linux-x86_64-2.6/./src/PyRcMisc.o build/temp.linux-x86_64-2.6/./src/PyRodsAdmin.o build/temp.linux-x86_64-2.6/./src/PyRodsDef.o build/temp.linux-x86_64-2.6/./src/PyRodsError.o build/temp.linux-x86_64-2.6/./src/PyRodsExec.o build/temp.linux-x86_64-2.6/./src/PyRodsFile.o build/temp.linux-x86_64-2.6/./src/PyRodsInfo.o build/temp.linux-x86_64-2.6/./src/PyRodsIO.o build/temp.linux-x86_64-2.6/./src/PyRodsLog.o build/temp.linux-x86_64-2.6/./src/PyRodsMeta.o build/temp.linux-x86_64-2.6/./src/PyRodsPath.o build/temp.linux-x86_64-2.6/./src/PyRodsQuery.o build/temp.linux-x86_64-2.6/./src/PyRodsStructFile.o build/temp.linux-x86_64-2.6/./src/PyRodsUser.o build/temp.linux-x86_64-2.6/./src/PyRodsXmsg.o build/temp.linux-x86_64-2.6/./src/PyStringOpr.o build/temp.linux-x86_64-2.6/./src/sqlMisc.o build/temp.linux-x86_64-2.6/./src/wrapper_misc.o /opt/irods/iRODS//server/core/obj/srvRodsAPIs.a /opt/irods/iRODS//lib/core/obj/libRodsAPIs.a /opt/irods/postgres/pgsql/lib/libodbc.a /opt/irods/iRODS//modules/properties/microservices/obj/propertiesMS.o /opt/irods/iRODS//modules/ERA/microservices/obj/eraUtil.o /opt/irods/iRODS//modules/ERA/microservices/obj/auditMS.o /opt/irods/iRODS//modules/ERA/microservices/obj/eraMS.o /opt/irods/iRODS//modules/ERA/microservices/obj/auditUtil.o /opt/irods/iRODS//modules/ERA/microservices/obj/collInfoMS.o /opt/irods/iRODS//modules/msoDrivers/microservices/obj/msoDboMS.o /opt/irods/iRODS//modules/msoDrivers/microservices/obj/msoHttpMS.o /opt/irods/iRODS//modules/msoDrivers/microservices/obj/msoSlinkMS.o /opt/irods/iRODS//modules/msoDrivers/microservices/obj/msoZ3950MS.o /opt/irods/iRODS//modules/msoDrivers/microservices/obj/msoIrodsMS.o /opt/irods/iRODS//modules/msoDrivers/microservices/obj/msoTestMS.o /opt/irods/iRODS//modules/msoDrivers/microservices/obj/msoSrbMS.o /opt/irods/iRODS//modules/examples/microservices/obj/examplesMS.o -lrt -lstdc++ -o build/lib.linux-x86_64-2.6/irods.so
g++: /opt/irods/iRODS//server/core/obj/srvRodsAPIs.a: No such file or directory
g++: /opt/irods/postgres/pgsql/lib/libodbc.a: Permission denied
Contributor

jhagberg commented Apr 20, 2012

Looks like you do not have read access in the postgres folder.

I have tried to build pyrods. Looks like we need to recompile postgres also...

I will give it a try.

Contributor

jhagberg commented Apr 20, 2012

I have now build PyRODS
following this
https://groups.google.com/d/msg/irod-chat/JMX3dqoeSXo/vyAeuQQl5DUJ

Changed the setup.py

Please have a look in
/opt/irods/PyRods-3.1.0

@jhagberg jhagberg closed this Apr 20, 2012

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brainstorm commented May 7, 2012

python setup.py build
(...)
g++: /opt/irods/postgres/pgsql/lib/libodbc.so: Permission denied
error: command 'g++' failed with exit status 1

Plus if you hit this error and know how to overcome it, followup on the thread:

https://groups.google.com/forum/?fromgroups&hl=sv#!topic/irod-chat/Y0vy7-0-RA8

@brainstorm brainstorm reopened this May 7, 2012

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brainstorm commented May 7, 2012

Different symbol is missing at uppmax:

(py2.7)[roman@u5 PyRods-3.1.0 0]$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/irods/postgres/pgsql/lib
(py2.7)[roman@u5 PyRods-3.1.0 0]$ python
Python 2.7 (r27:82500, Sep  7 2010, 13:19:24) 
[GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import irods
Traceback (most recent call last):
  File "", line 1, in 
ImportError: roman/.virtualenvs/py2.7/lib/python2.7/site-packages/irods.so: undefined symbol: rcSubStructFileRmdir
Contributor

brainstorm commented May 7, 2012

From PyRODS README:

  You will have an error when you try to do import irods in a python shell
  after installing the package, it will complain for a missing object file for
  the module.
  If all goes well the script parses the config.mk file in the irods directory
  to find which module is linked with the server. It assumes a standard
  hierarchy (modules/modulename/obj/*.o), if this is not the case you will
  have to modify the script.
Contributor

brainstorm commented May 8, 2012

@jhagberg did:

I disabled GSI_auth
make clean
make
rm * in Pyrods build
python setup.py build

And worked.

@brainstorm brainstorm closed this May 8, 2012

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