tutorial_1_installing

[Eligiusz Postek]

Dear Colleagues,
I do not see the Makefile.common, therefore

declare -x LD_LIBRARY_PATH="/apl/tryton/boost/gcc/1.6.2/lib:/apl/tryton/openmpi/1.10.2-gcc5/lib:/apl/tryton/python/2.7.11/lib:/apl/tryton/gcc/5.4.0/lib64:/users/kdm/ewpostek/bioc2/tbb/tbb2017_20170604oss/lib/intel64/gcc4.4"

I have the loaded modules: Currently Loaded Modulefiles:
  1) tryton/compiler/gcc/5.4.0        4) tryton/mpi/openmpi/1.10.2-gcc5
  2) tryton/python2/2.7.11            5) tryton/boost/gcc/1.6.2
  3) tryton/swig/3.0.8

I build the libmodel.DP.SPAGENT.so
This is my root --- #BIOCELLION_ROOT = /home/kang697/BIOCELLION/biocellion
                             BIOCELLION_ROOT = /users/kdm/ewpostek/bioc2/BIOCELLION_RELEASE/biocellion

The first model is here:

ewpostek@tryton-ap:~/bioc2/BIOCELLION_RELEASE/biocellion-user/1_building_the_first_model$ ls
interface_agent.o        libmodel.DP.SPAGENT.so    model_routine_config.o         model_routine_output.o
interface_check.o        Makefile                  model_routine_grid.cpp         output
interface_config.o       model_define.h            model_routine_grid.o           tutorial.xml
interface_grid.o         model_routine_agent.cpp   model_routine_mech_intrct.cpp  zz
interface_mech_intrct.o  model_routine_agent.o     model_routine_mech_intrct.o
interface_output.o       model_routine_config.cpp  model_routine_output.cpp
ewpostek@tryton-ap:~/bioc2/BIOCELLION_RELEASE/biocellion-user/1_building_the_first_model$ pwd
/users/kdm/ewpostek/bioc2/BIOCELLION_RELEASE/biocellion-user/1_building_the_first_model
ewpostek@tryton-ap:~/bioc2/BIOCELLION_RELEASE/biocellion-user/1_building_the_first_model$

However, I get the error:

ewpostek@tryton-ap:~/bioc2/BIOCELLION_RELEASE/biocellion-user/1_building_the_first_model$ /users/kdm/ewpostek/bioc2/BIOCELLION_RELEASE/biocellion/framework/main/biocellion.DP.SPAGENT.OPT  tutorial.xml
/users/kdm/ewpostek/bioc2/BIOCELLION_RELEASE/biocellion/framework/main/biocellion.DP.SPAGENT.OPT: error while loading shared libraries: libmodel.DP.SPAGENT.so: cannot open shared object file: No such file or directory

This is my system:

cat /proc/version
Linux version 2.6.32-696.3.2.el6.x86_64 (mock...@c1bl.rdu2.centos.org) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) )

Could you be so kind to give a hint ?

Best regards, Elek

[seunghwa.kang]

I assume you downloaded Biocellion 1.2 and are you referencing the Biocellion 1.2. manual?

Biocellion does not use Makefile.common in version 1.2.

And I am worried that you're seeing the instructions for Biocellion 1.1.

-seunghwa

[seunghwa.kang]

See Section 6.2.1 in http://biocellion.com/documentation/Biocellion-1.2.pdf

-seunghwa

On Thursday, June 29, 2017 at 1:54:13 AM UTC-7, Eligiusz Postek wrote:

[Eligiusz Postek]

Hi,
I took the instructions from wiki on the *com page.

However, I looked into the right documentation,
but I still have the problem;
 This is my model dir:

ewpostek@tryton-ap:~/bioc2/my_biocellion_user/model$ ls

interface_agent.o        libmodel.DP.SPAGENT.so    model_routine_config.o         model_routine_output.o
interface_check.o        Makefile                  model_routine_grid.cpp         output
interface_config.o       model_define.h            model_routine_grid.o           tutorial.xml
interface_grid.o         model_routine_agent.cpp   model_routine_mech_intrct.cpp  zz
interface_mech_intrct.o  model_routine_agent.o     model_routine_mech_intrct.o
interface_output.o       model_routine_config.cpp  model_routine_output.cpp

ewpostek@tryton-ap:~/bioc2/my_biocellion_user/model$ pwd
/users/kdm/ewpostek/bioc2/my_biocellion_user/model
ewpostek@tryton-ap:~/bioc2/my_biocellion_user/model$

This is my upper dir:
ewpostek@tryton-ap:~/bioc2/my_biocellion_user$ ls
biocellion  biocellion-user  libmodel  Makefile.model  model
ewpostek@tryton-ap:~/bioc2/my_biocellion_user$

in the Makefile.model  I set  BIOCELLION_ROOT = /users/kdm/ewpostek/bioc2/my_biocellion_user/biocellion

There is main: BIOCELLION_ROOT = /users/kdm/ewpostek/bioc2/my_biocellion_user/biocellion

and still the problem:
ewpostek@tryton-ap:~/bioc2/my_biocellion_user/model$ /users/kdm/ewpostek/bioc2/my_biocellion_user/biocellion/framework/main/biocellion.DP.SPAGENT.MPI.DEBUG   tutorial.xml
/users/kdm/ewpostek/bioc2/my_biocellion_user/biocellion/framework/main/biocellion.DP.SPAGENT.MPI.DEBUG: error while loading shared libraries: libmodel.DP.SPAGENT.so: cannot open shared object file: No such file or directory
ewpostek@tryton-ap:~/bioc2/my_biocellion_user/model$

Could you help,
reards,
Elek

[seunghwa.kang]

error while loading shared libraries: libmodel.DP.SPAGENT.so: cannot open shared object file: No such file or directory

=>
This is because LD_LIBRARY_PATH is not properly set.

See Section 6.4 in http://biocellion.com/documentation/Biocellion-1.2.pdf

You need to update LD_LIBRARY_PATH to point both the model directory (where libmodel.DP.SPAGENT.so is) and the TBB library directory. Let me know if you need further clarification.

-seunghwa

On Thursday, June 29, 2017 at 1:54:13 AM UTC-7, Eligiusz Postek wrote:

[Eligiusz Postek]

Thank you, it works very well,
Elek