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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoPlainText>Hi there,<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>I have some questions about BLAS and LAPACK in Gromacs, and how to best call these functions from inside my code. <o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>On my local machine, I migrated my fluctuating charge code from Gromacs 4.0.7 to 4.5.5. It took a bit of time, but I think the implementation is now a lot cleaner. At some point, I would like to create a branch on the Gromacs repository, but first I need to solve a few issues with BLAS and LAPACK. Basically, when I was originally writing the code I used the Intel headers and libraries, but now I want to convert this to something more compatible.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>At the top of my code, I have the following two includes:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><span style='font-family:"Courier New"'>#include <mkl_cblas.h><o:p></o:p></span></p><p class=MsoPlainText><span style='font-family:"Courier New"'>#include <mkl_lapack.h><o:p></o:p></span></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>When I build the executables, I need to source the Intel compiler variables and make sure to link with the following line:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><span style='font-family:"Courier New"'>LDFLAGS="-lrt -L$INTEL_PATH/lib/intel64 -L$MKLROOT/lib/em64t -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm"<o:p></o:p></span></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>I understand this needs to be changed. I would prefer to use the BLAS and LAPACK provided by Gromacs, but I don't know how to do this most effectively, and whether this will result in a performance hit.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>In my code I call the BLAS and LAPACK functions like this (there are perhaps 100 such calls):<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><span style='font-family:"Courier New"'>cblas_dgemm(101,111,111,N,N,N,1,VT,N,A1,N,0,Ai,N);<o:p></o:p></span></p><p class=MsoPlainText><span style='font-family:"Courier New"'>dgelss(&N,&N,&nrhs,A1,&N,x,&N,S,&rcond,&rank,work,&lwork,&info); <o:p></o:p></span></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>However, when Gromacs calls its own BLAS and LAPACK functions it looks quite different:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><span style='font-family:"Courier New"'>#ifdef GMX_DOUBLE<o:p></o:p></span></p><p class=MsoPlainText><span style='font-family:"Courier New"'> F77_FUNC(dsyevr,DSYEVR)(jobz,"I","L",&n,a,&n,&vl,&vu,&index_lower,&index_upper,<o:p></o:p></span></p><p class=MsoPlainText><span style='font-family:"Courier New"'> &abstol,&m,eigenvalues,eigenvectors,&n,<o:p></o:p></span></p><p class=MsoPlainText><span style='font-family:"Courier New"'> isuppz,&w0,&lwork,&iw0,&liwork,&info);<o:p></o:p></span></p><p class=MsoPlainText><span style='font-family:"Courier New"'>#else<o:p></o:p></span></p><p class=MsoPlainText><span style='font-family:"Courier New"'> F77_FUNC(ssyevr,SSYEVR)(jobz,"I","L",&n,a,&n,&vl,&vu,&index_lower,&index_upper,<o:p></o:p></span></p><p class=MsoPlainText><span style='font-family:"Courier New"'> &abstol,&m,eigenvalues,eigenvectors,&n,<o:p></o:p></span></p><p class=MsoPlainText><span style='font-family:"Courier New"'> isuppz,&w0,&lwork,&iw0,&liwork,&info);<o:p></o:p></span></p><p class=MsoPlainText><span style='font-family:"Courier New"'>#endif<o:p></o:p></span></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>The only example I could find for this function call is in “tools/eigensolver.c” . I’m worried that conversion will be difficult, plus I would like to retain the option to use the Intel libraries. <o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>My questions are:<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText style='margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span style='mso-list:Ignore'>1)<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]>How can I most effectively convert my BLAS / LAPACK calls in qtpie.c so that it uses the Gromacs provided libraries? (<a href="https://dl.dropbox.com/u/5381783/qtpie.c">link</a>)<o:p></o:p></p><p class=MsoPlainText style='margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span style='mso-list:Ignore'>2)<span style='font:7.0pt "Times New Roman"'> </span></span><![endif]>How should I write my code so that a user can compile and link using Intel headers / libraries if they want to? I imagine it’s related to the --use-external-blas and --use-external-lapack command line options to the configure script, but I don’t know how to use this.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Your response is greatly appreciated.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Thanks,<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>- Lee-Ping<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>