Problems compiling fcma-toolbox

[acamargofb]

I am having problems compiling the fcma-toolbox
I did the following:

1. sudo cmake CMakeList.txt
2. sudo make
   and I got the following errors:
   ..
   .
   .
   [ 82%] Building CXX object CMakeFiles/FCMA.dir/src/FisherScoring.cc.o
   [ 86%] Building CXX object CMakeFiles/FCMA.dir/src/LibSVM.cc.o
   [ 91%] Building CXX object CMakeFiles/FCMA.dir/src/main.cc.o
   [ 95%] Building CXX object CMakeFiles/FCMA.dir/src/Marginal_Scheduler.cc.o
   [100%] Linking CXX executable FCMA
   CMakeFiles/FCMA.dir/src/Scheduler.cc.o: In function DoSlave(int, int, trial_data_t*, trial_data_t*, Task, trial_t*, int, int, int, int, int)': Scheduler.cc:(.text+0x124): undefined reference to ompi_mpi_comm_world'
   Scheduler.cc:(.text+0x12b): undefined reference to ompi_mpi_int' Scheduler.cc:(.text+0x189): undefined reference to MPI_Recv'
   Scheduler.cc:(.text+0x190): undefined reference to MPI_Wtime' Scheduler.cc:(.text+0x1ec): undefined reference to MPI_Wtime'
   Scheduler.cc:(.text+0x1fd): undefined reference to ompi_mpi_float' Scheduler.cc:(.text+0x221): undefined reference to MPI_Send'
   Scheduler.cc:(.text+0x23e): undefined reference to MPI_Send' Scheduler.cc:(.text+0x249): undefined reference to ompi_mpi_float'
   Scheduler.cc:(.text+0x25f): undefined reference to MPI_Send' Scheduler.cc:(.text+0x2e9): undefined reference to MPI_Wtime'
   Scheduler.cc:(.text+0x2fa): undefined reference to ompi_mpi_float' Scheduler.cc:(.text+0x321): undefined reference to MPI_Send'
   Scheduler.cc:(.text+0x33e): undefined reference to `MPI_Send'
   .
   .
   .

Does somebody know how to fix this issue ?

Have a nice day,

Aldo

[yidawang]

It looks like that your system doesn't have MPI packages.
I would recommend you check out the FCMA component of BrainIAK, which has better support and should be easier to install and run.

[acamargofb]

Do you know or someone how to solve the issue with the MPI packages. I have installed with sudo apt-get install and also from the code with configure
Best,
Aldo

[yidawang]

You may check if the MPI library is correctly linked while compiling FCMA. It seems to me that the system doesn't find corresponding libraries even if you have installed somewhere.

[acamargofb]

Hi Yida Wang:

I solved the problem of compilation, I have to change the CMakeFile.txt, this part:
...
set (EXTRA_LIBS ${EXTRA_LIBS} svmphi svmsimple niftiio znz mpi OpenCL blas openblas boost_system hdf5_serial boost_iostreams z hdf5_serial_hl boost_serialization boost_mpi)

...

Best regards,

Aldo

[acamargofb]

Hi Yida:

I have a question:

I would like to use this toolbox to do a correlation between tfn and rfn defined like this:

tfn = 'aal_tpl.nii'; % ROI filename
rfn = 'swrfunc.nii'; % resting state fMRI

How can I do that with this toolbox?

Thanks a lot in advance,

Aldo

[yidawang]

Aldo,

If you would like to leverage HPC to do some correlation computation quickly, I would recommend you to refer to FCMA@BrainIAK again. We have example code for high-performance correlation computation at https://github.com/IntelPNI/brainiak/blob/master/examples/fcma/corr_comp.py

Hope it helps,
Yida