Installation issue

[bmdeen]

Hi,

I'm running into difficulties trying to install msm on a Linux system (CentOS 7.9.2009, amd64, GCC 4.8.5, FSL 6.0.1). When I run the precompiled CentOS binaries, I get a "cannot execute binary file" error. When I try to compile the DiscreteOpt package using make, I get the below error:

c++ -Wall -ansi -pedantic -Wno-long-long     -g -DNDEBUG -std=c++11  -DHAS_HOCR  -DNDEBUG -m64  -g -O3 -fexpensive-optimizations -m64  -I/lab_files/opt/fsl-6.0.1/extras/include/boost -I/lab_files/opt/fsl-6.0.1/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -DARMA_64BIT_WORD -I/lab_files/opt/fsl-6.0.1/extras/include/newran -I/usr/include -I/lab_files/opt/fsl-6.0.1/extras/include/libcprob -I/lab_files/opt/fsl-6.0.1/extras/include/libprob -I/lab_files/opt/fsl-6.0.1/extras/include/boost -I/bdeen/scripts/MSM/include -I/bdeen/scripts/MSM/extras/include -I. -I/bdeen/scripts/MSM/include -I/lab_files/opt/fsl-6.0.1/include   -c -o DiscreteCostFunction.o DiscreteCostFunction.cpp
DiscreteCostFunction.cpp: In member function ‘virtual double DISCRETEOPT::NonLinearSRegDiscreteCostFunction::computeTripletCost(int, int, int, int)’:
DiscreteCostFunction.cpp:434:107: error: no matching function for call to ‘calculate_triangular_strain(NEWMESH::Triangle&, NEWMESH::Triangle&, float&, float&, boost::shared_ptr<armawrap::AWColVector<double> >, float&)’
     cost=calculate_triangular_strain(TRI_ORIG, TRI, _mu, _kappa, boost::shared_ptr<ColumnVector>(), _k_exp);
                                                                                                           ^
DiscreteCostFunction.cpp:434:107: note: candidates are:
In file included from /lab_files/opt/fsl-6.0.1/include/newmesh/featurespace.h:77:0,
                 from similarities.h:17,
                 from DiscreteCostFunction.h:9,
                 from DiscreteCostFunction.cpp:8:
/lab_files/opt/fsl-6.0.1/include/newmesh/meshfns.h:123:10: note: double NEWMESH::calculate_triangular_strain(const NEWMESH::Triangle&, const NEWMESH::Triangle&, const double&, const double&, const boost::shared_ptr<armawrap::AWColVector<double> >&)
   double calculate_triangular_strain(const Triangle &,const Triangle &,const double &,const double &, const boost::shared_ptr<ColumnVector> & indexSTRAINS=boost::shared_ptr<ColumnVector> ());
          ^
/lab_files/opt/fsl-6.0.1/include/newmesh/meshfns.h:123:10: note:   candidate expects 5 arguments, 6 provided
/lab_files/opt/fsl-6.0.1/include/newmesh/meshfns.h:125:10: note: double NEWMESH::calculate_triangular_strain(int, const NEWMESH::newmesh&, const NEWMESH::newmesh&, const double&, const double&, const boost::shared_ptr<armawrap::AWColVector<double> >&)
   double calculate_triangular_strain(int, const NEWMESH::newmesh &, const NEWMESH::newmesh &,const double &,const double &, const boost::shared_ptr<ColumnVector> & indexSTRAINS=boost::shared_ptr<ColumnVector> ());
          ^
/lab_files/opt/fsl-6.0.1/include/newmesh/meshfns.h:125:10: note:   no known conversion for argument 1 from ‘NEWMESH::Triangle’ to ‘int’
DiscreteCostFunction.cpp:497:111: error: no matching function for call to ‘calculate_triangular_strain(NEWMESH::Triangle&, NEWMESH::Triangle&, float&, float&, boost::shared_ptr<armawrap::AWColVector<double> >, float&)’
    cost+=calculate_triangular_strain(TRIorig, TRItrans, _mu, _kappa, boost::shared_ptr<ColumnVector>(), _k_exp);
                                                                                                               ^
DiscreteCostFunction.cpp:497:111: note: candidates are:
In file included from /lab_files/opt/fsl-6.0.1/include/newmesh/featurespace.h:77:0,
                 from similarities.h:17,
                 from DiscreteCostFunction.h:9,
                 from DiscreteCostFunction.cpp:8:
/lab_files/opt/fsl-6.0.1/include/newmesh/meshfns.h:123:10: note: double NEWMESH::calculate_triangular_strain(const NEWMESH::Triangle&, const NEWMESH::Triangle&, const double&, const double&, const boost::shared_ptr<armawrap::AWColVector<double> >&)
   double calculate_triangular_strain(const Triangle &,const Triangle &,const double &,const double &, const boost::shared_ptr<ColumnVector> & indexSTRAINS=boost::shared_ptr<ColumnVector> ());
          ^
/lab_files/opt/fsl-6.0.1/include/newmesh/meshfns.h:123:10: note:   candidate expects 5 arguments, 6 provided
/lab_files/opt/fsl-6.0.1/include/newmesh/meshfns.h:125:10: note: double NEWMESH::calculate_triangular_strain(int, const NEWMESH::newmesh&, const NEWMESH::newmesh&, const double&, const double&, const boost::shared_ptr<armawrap::AWColVector<double> >&)
   double calculate_triangular_strain(int, const NEWMESH::newmesh &, const NEWMESH::newmesh &,const double &,const double &, const boost::shared_ptr<ColumnVector> & indexSTRAINS=boost::shared_ptr<ColumnVector> ());
          ^
/lab_files/opt/fsl-6.0.1/include/newmesh/meshfns.h:125:10: note:   no known conversion for argument 1 from ‘NEWMESH::Triangle’ to ‘int’
DiscreteCostFunction.cpp:343:8: warning: unused variable ‘filename’ [-Wunused-variable]
   char filename[1000];
        ^
make: *** [DiscreteCostFunction.o] Error 1

Any idea what's going wrong, either with the binary file or the compilation? Thanks!

[ecr05]

Hi, did you compile all the subfolders? You'll also need to recompile the FastPD folder in the FSL folder. Have you reviewed the step by step guidance in https://github.com/ecr05/MSM_HOCR/blob/master/compilation%20instructions?

Thanks

Emma

[bmdeen]

Hi Emma,

I'm following those instructions. The first folder I tried to compile was DiscreteOpt, and I get the errors above during that step. Thanks,

Ben

[ecr05]

Well the obvious but unhelpful answer is that the version of newmesh from your fsl6 is incompatible but I don't immediately know why since the fsl 6 version I have seems to have it. Can you post to the FSL list so I can discuss with them?

[bmdeen]

Problem solved - I needed to use version 6.0.2 or greater of FSL, and copy the binaries to $FSLDIR/bin before using. Thanks for your help!