Executable biocellion

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Dvory Shait

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May 20, 2019, 7:11:38 AM5/20/19

to Biocellion Support

Hello,

I am IT, and would like to install biocellion for a user.

I have been following the instructions in http://documentation.biocellion.com/documentation/Biocellion-1.2.pdf, and installed biocellion with TBB.

I tried to run it with an example, as stated in http://wiki.biocellion.com/index.php/Building_the_First_Model, and the 'make' command succeeded to create DP.SPAGENT.OPT.so file.

However, this is not an executable file, so I am not quite sure how this file is supposed to be generated.

Please see below my history, OS is centos7

999 cd /powerapps/share/src

1004 mkdir biocellion

1005 cd biocellion/

1006 tar -xf /tmp/biocellion.1.2.rc.gcc5.x.12.20.2016.tar.gz

1007 ls

1008 cd BIOCELLION_RELEASE/

1013 mv biocellion-user/Makefile.model{,.org}

1014 cp biocellion/libmodel/Makefile.model biocellion-user/.

1015 cp -rf biocellion/libmodel/model biocellion-user/.

1017 vi biocellion-user/Makefile.model

Add the change:

BIOCELLION_ROOT = /powerapps/share/src/biocellion/BIOCELLION_RELEASE/biocellion

1021 cd biocellion-user/

1023 cd model

1025 module load gcc/gcc-8.2.0

1026 make

Then I did what was suggested in http://wiki.biocellion.com/index.php/Building_the_First_Model

Copied the example directory to biocellion-user:

[root@power8 biocellion-user]# pwd

/powerapps/share/src/biocellion/BIOCELLION_RELEASE/biocellion-user

[root@power8 biocellion-user]# ls

1_building_the_first_model 4_grid_molecular_concentration_non_ode model

2_cell_growth_and_cell_death LICENSE model-gut

2_cell_growth_and_cell_death_ODE_Version Makefile.model model.org

3_mechanical_interactions Makefile.model.org model-sorting

[root@power8 biocellion-user]#

Copied .cpp and h files to BIOCELLION_RELEASE/biocellion/libmodel

and did 'make'. Compilation succeeded, with no executable being generated

[root@power8 model]# pwd

/powerapps/share/src/biocellion/BIOCELLION_RELEASE/biocellion/libmodel/model

[root@power8 model]# make

g++ -shared -Wl,-soname,libmodel.DP.SPAGENT.so -o libmodel.DP.SPAGENT.so interface_config.o interface_agent.o interface_mech_intrct.o interface_grid.o interface_output.o model_routine_config.o model_routine_grid.o model_routine_agent.o model_routine_mech_intrct.o model_routine_output.o interface_check.o

[root@power8 model]# make clean

rm -f *.ilo

rm -f *.o

rm -f *.so

[root@power8 model]# make

g++ -g -Wall -DTHIS_IS_LIBMODEL=1 -DDIMENSION=3 -DREAL_IS_FLOAT=0 -DHAS_MPAGENT=0 -DHAS_SPAGENT=1 -DENABLE_CHECK=1 -fPIC -I /powerapps/share/src/biocellion/BIOCELLION_RELEASE/biocellion/include -I /powerapps/share/src/biocellion/BIOCELLION_RELEASE/biocellion/include -I /powerapps/share/src/biocellion/BIOCELLION_RELEASE/biocellion/libmodel/include -c /powerapps/share/src/biocellion/BIOCELLION_RELEASE/biocellion/libmodel/interface/interface_config.cpp -o interface_config.o

g++ -g -Wall -DTHIS_IS_LIBMODEL=1 -DDIMENSION=3 -DREAL_IS_FLOAT=0 -DHAS_MPAGENT=0 -DHAS_SPAGENT=1 -DENABLE_CHECK=1 -fPIC -I /powerapps/share/src/biocellion/BIOCELLION_RELEASE/biocellion/include -I /powerapps/share/src/biocellion/BIOCELLION_RELEASE/biocellion/include -I /powerapps/share/src/biocellion/BIOCELLION_RELEASE/biocellion/libmodel/include -c model_routine_mech_intrct.cpp -o model_routine_mech_intrct.o

[root@power8 model]# ls -lart

total 8260

-rw-r--r-- 1 root root 2963 May 20 12:05 Makefile

-rw-r--r-- 1 root root 6757 May 20 12:06 model_routine_agent.cpp

-rw-r--r-- 1 root root 8859 May 20 12:06 model_routine_config.cpp

-rw-r--r-- 1 root root 8834 May 20 12:06 model_routine_grid.cpp

-rw-r--r-- 1 root root 2608 May 20 12:06 model_routine_mech_intrct.cpp

-rw-r--r-- 1 root root 2786 May 20 12:06 model_routine_output.cpp

-rw-r--r-- 1 root root 3277 May 20 12:06 model_define.h

drwxr-xr-x 6 2898 users 4096 May 20 12:19 ..

-rw-r--r-- 1 root root 754760 May 20 14:10 interface_config.o

-rw-r--r-- 1 root root 691336 May 20 14:10 interface_agent.o

-rw-r--r-- 1 root root 378816 May 20 14:10 interface_mech_intrct.o

-rw-r--r-- 1 root root 568408 May 20 14:10 interface_grid.o

-rw-r--r-- 1 root root 530048 May 20 14:10 interface_output.o

-rw-r--r-- 1 root root 1033888 May 20 14:10 model_routine_config.o

-rw-r--r-- 1 root root 367200 May 20 14:10 model_routine_grid.o

-rw-r--r-- 1 root root 816912 May 20 14:10 model_routine_agent.o

-rw-r--r-- 1 root root 322392 May 20 14:10 model_routine_mech_intrct.o

-rw-r--r-- 1 root root 360976 May 20 14:10 model_routine_output.o

-rw-r--r-- 1 root root 104632 May 20 14:10 interface_check.o

drwxr-xr-x 2 root root 4096 May 20 14:10 .

-rwxr-xr-x 1 root root 2389664 May 20 14:10 libmodel.DP.SPAGENT.so

[root@power8 model]#

Compiler is gcc-8.2.0

Would appreciate your help, thanks

Dvory

Chris K

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May 20, 2019, 11:50:33 AM5/20/19

to Biocellion Support

Hi Dvory,

Under your /biocellion/framework/main directory, you should see Biocellion executables (which comes with the .tar.gz you downloaded) such as biocellion.DP.SPAGENT.OPT .

Try running the executable with the tutorial.xml that comes with each tutorial model:

       /LOCATION_OF_BIOCELLION_ROOT/framework/main/DP.SPAGENT.OPT tutorial.xml