cannot find blas/lapack #112

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1. krrutkow commented on Oct 14, 2022

   

   krrutkow

   on Oct 14, 2022

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   It seems that (on my system anyways) multifario is somewhat improperly configured. The libMF references symbols from libSH, but it is not linked to it and assumes the user of the libraries links to them both. The problem this causes for Julia is that it is not linked to the libraries, it loads them dynamically, and the default behavior is to keep dynamically loaded libraries from accessing each other.

   So a quick fix I did was to make a single library to link all of the multifario libraries together, like the gcc command does:

   gcc -g -O -I./include -DNOMFSIMPLEX -DMFALLOWVERBOSE -DMANIFOLD -DHAVE_AUTO -g -O2 -shared -o libmultifario.so -L./lib lib/.libs/libMF.so lib/.libs/libExpCmp.so lib/.libs/libSH.so lib/.libs/libauto2000.so lib/.libs/libautof2c.so -llapack -lblas -L/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/11.2.0/../../.. -lgfortran -lquadmath -lm -ltiff -Wl,-rpath -Wl,$PWD/multifario-v1.0/usr/lib
   

   Which is essentially the command used to build ComputeSphereSub (found by running make), but using -shared -o libmultifario.so in place of -o bin/.libs/ComputeSphereSub Examples/ComputeSphereSub.o in that command.

   This 1 library can then be used, something like this:

   julia> module libmultifario
          using CBinding
          c`-I $(pwd())/multifario-v1.0/include -L $(pwd())/multifario-v1.0 -lmultifario`
          const c"FILE" = Cvoid
   
          # headers included from ComputeSphereSub.c
          c"""
          #include <MFAtlas.h>
          #include <MFNRegion.h>
          #include <MFNVector.h>
          #include <MFFortran.h>
          #include <MFMultifariosMethod.h>
          """ji
          end

   There are many warnings about functions defined in the header files that are not actually in the libraries though, but it seems that implementing the ComputeSphereSub code in Julia is possible:

   julia> e=libmultifario.MFCreateErrorHandler()
   CBinding.Cptr{Main.libmultifario.var"c\"struct MFErrorHandlerSt\""}(0x0000000001ec49d0)

   At no point did I encounter an issue with BLAS/LAPACK as you mentioned though, so perhaps this alternative approach mitigates that issue for you.
2. rveltz commented on Oct 14, 2022

   

   rveltz

   on Oct 14, 2022

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   Thanks a lot for the explanations! I still have the same issue (julia 1.8 apple M1). The last line output the lapack error

   c"""
   #include <MFFortran.h>
   #include <multifarioConfig.h>
   #include <MFAtlas.h>
   #include <MFNRegion.h>
   #include <MFNVector.h>
   #include <math.h>
   #include <MFFortran.h>
   #include <MFMultifariosMethod.h>
   """ji
   
   function F(n, z, m, f, data, e)
       f[1]= z[1]^2 + z[2]^2 + z[3]^2 - 1.
       nothing
   end
   
   function dF(n, z, m, df, data, e)
       df[0+1* 0+1]= 2*z[0+1]
       df[0+1* 1+1]= 2*z[1+1]
       df[0+1* 2+1]= 2*z[2+1]
       nothing
   end
   
   function ddF(n, z, m, ddf, data, e)
       ddf[0+1*(0+3*0)+1]= 2
       ddf[0+1*(1+3*0)+1]= 0
       ddf[0+1*(2+3*0)+1]= 0
   
       ddf[0+1*(0+3*1)+1]= 0
       ddf[0+1*(1+3*1)+1]= 2
       ddf[0+1*(2+3*1)+1]= 0
   
       ddf[0+1*(0+3*2)+1]= 0
       ddf[0+1*(1+3*2)+1]= 0
       ddf[0+1*(2+3*2)+1]= 2
       nothing
   end
   
   function DrawSphere( v,u,d, e)
     if(u==C_NULL||v==C_NULL)
       return Int32(3)
     end
   
     u[0+1] = MFNV_C(v,0,e)
     u[1+1] = MFNV_C(v,1,e)
     u[2+1] = MFNV_C(v,2,e)
   
     return Int32(0)
   end
   
   e = MFCreateErrorHandler()
   n = 3
   k = 2
   M = MFIMFCreateAlgebraicSubroutine(n, k, F, dF, ddF, C_NULL, e)
   
   MFIMFSetProjectForDraw(M, DrawSphere, e)
   
   u0 = [MFIMFVectorFactory(M, e) for _ = 1:2]
   
   Omega = MFNRegionCreateHyperCube(n, 1.1, e)
   
   u0[1] = MFIMFVectorFactory(M, e)
   for j=0:n-1
       MFNVSetC(u0[1], j, 0., e)
   end
   MFNVSetC(u0[1], 1, 1., e)
   
   u0[2]=MFIMFVectorFactory(M, e)
   for j=0:n-1
       MFNVSetC(u0[2], j, 0., e)
   end
   MFNVSetC(u0[2], 2, 1., e)
   
   H = MFCreateMultifariosMethod(e)
   MFMultifarioSetRealParameter(H, "epsilon", .01, e)
   MFMultifarioSetIntegerParameter(H, "maxCharts", 100, e)
   MFMultifarioSetIntegerParameter(H, "verbose", 1, e)
   MFMultifarioSetIntegerParameter(H, "page", 1, e)
   MFMultifarioSetIntegerParameter(H, "dumpToPlotFile", 1, e)
   MFMultifarioSetIntegerParameter(H, "dumpToCenterFile", 1, e)
   MFMultifarioSetFilename(H, "SphereSub", e)
   
   S = MFComputeAtlasMultiple(H, M, Omega, 2, u0, e)
3. krrutkow commented on Oct 14, 2022

   

   krrutkow

   on Oct 14, 2022

   Last edited by krrutkow

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   Well, unfortunately what you posted runs fine on my Linux system with Julia 1.8.2... Only thought I have is to just verify that your aggregate library links to some BLAS/LAPACK libraries. It might look something like this (run in a shell):

   ldd multifario-v1.0/libmultifario.so 
           linux-vdso.so.1 (0x00007ffdc1791000)
           libMF.so.0 => multifario-v1.0/usr/lib/libMF.so.0 (0x00007f709b8fa000)
           libExpCmp.so.0 => multifario-v1.0/usr/lib/libExpCmp.so.0 (0x00007f709b8ea000)
           libSH.so.0 => multifario-v1.0/usr/lib/libSH.so.0 (0x00007f709b8d7000)
           libauto2000.so.0 => multifario-v1.0/usr/lib/libauto2000.so.0 (0x00007f709b886000)
           libautof2c.so.0 => multifario-v1.0/usr/lib/libautof2c.so.0 (0x00007f709b881000)
           liblapack.so.3 => /usr/lib/liblapack.so.3 (0x00007f709b16d000)
           libopenblas.so.3 => /usr/lib/libopenblas.so.3 (0x00007f7099db8000)
           libgfortran.so.5 => /usr/lib/libgfortran.so.5 (0x00007f7099afd000)
           libquadmath.so.0 => /usr/lib/libquadmath.so.0 (0x00007f7099ab2000)
           libm.so.6 => /usr/lib/libm.so.6 (0x00007f70999ca000)
           libtiff.so.5 => /usr/lib/libtiff.so.5 (0x00007f7099936000)
           libc.so.6 => /usr/lib/libc.so.6 (0x00007f709972c000)
           libgcc_s.so.1 => /usr/lib/libgcc_s.so.1 (0x00007f7099711000)
           libgomp.so.1 => /usr/lib/libgomp.so.1 (0x00007f70996cc000)
           /usr/lib64/ld-linux-x86-64.so.2 (0x00007f709b9ca000)
           libzstd.so.1 => /usr/lib/libzstd.so.1 (0x00007f709961d000)
           liblzma.so.5 => /usr/lib/liblzma.so.5 (0x00007f70995f4000)
           libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0x00007f7099573000)
           libz.so.1 => /usr/lib/libz.so.1 (0x00007f7099559000)
           libpthread.so.0 => /usr/lib/libpthread.so.0 (0x00007f7099554000)