Thread: [Apbs-users] compiling error on AMD64 cluster
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From: Xiaoqing W. <kit...@12...> - 2005-06-16 10:23:28
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Hi, I compile APBS following the "Source installation" section of user-guide on amd64 cluster. The "make" error as follows -------------------------------------------------------- pgf77 -O2 -fPIC -fastsse -Bstatic -o apbslibc.so -shared apbslib.o ../../bin/.libs/libapbsmainroutines.a ../../src/aaa_lib/.libs/libapbs.a -L/home/xqwang/apbs/apbs-0.3.2/lib -L/home/xqwang/apbs/soft/lib/x86_64-unknown-linux -lmaloc -L/usr/lib64 -lblas -L/usr/local/mpich_pg/lib -lmpich -lm -lreadline -lncurses /usr/bin/ld: /usr/local/mpich_pg/lib/libmpich.a(isend.o): relocation R_X86_64_32 can not be used when making a shared object; recompile with -fPIC /usr/local/mpich_pg/lib/libmpich.a: could not read symbols: Bad value make[2]: *** [apbslibc.so] Error 2 make[2]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools/python' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools' ------------------------------------------------------------------ I run "./configure --help" and find that optional features "--enable-static=PKGS build static libraries default=yes". Why it makes shared object? How can I solve this problem? Any tips would be greatly appreciated! Sincerely, Xiaoqing |
From: Nathan B. <sob...@ya...> - 2005-06-16 19:50:57
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This is a strange error -- I don't know why the code was being compiled into shared libraries. Can you send me the environmental variables and configure command you used? Thanks, Nathan --- Xiaoqing Wang <kit...@12...> wrote: > Hi, > I compile APBS following the "Source installation" section of > user-guide on amd64 cluster. > The "make" error as follows > -------------------------------------------------------- > pgf77 -O2 -fPIC -fastsse -Bstatic -o apbslibc.so -shared apbslib.o > ../../bin/.libs/libapbsmainroutines.a > ../../src/aaa_lib/.libs/libapbs.a > -L/home/xqwang/apbs/apbs-0.3.2/lib > -L/home/xqwang/apbs/soft/lib/x86_64-unknown-linux -lmaloc -L/usr/lib64 > -lblas -L/usr/local/mpich_pg/lib -lmpich -lm -lreadline > -lncurses > > /usr/bin/ld: /usr/local/mpich_pg/lib/libmpich.a(isend.o): relocation > R_X86_64_32 can not be used when making a shared object; recompile with > -fPIC > /usr/local/mpich_pg/lib/libmpich.a: could not read symbols: Bad value > make[2]: *** [apbslibc.so] Error 2 > make[2]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools/python' > make[1]: *** [all-recursive] Error 1 > make[1]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools' > ------------------------------------------------------------------ > > I run "./configure --help" and find that optional features > "--enable-static=PKGS build static libraries default=yes". Why it makes > shared object? > > How can I solve this problem? > > Any tips would be greatly appreciated! > > Sincerely, > Xiaoqing > > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu |
From: Xiaoqing W. <kit...@12...> - 2005-06-17 04:35:31
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Hi, The environmental variables and configure commands as follows: ----------------------------------------------------------------- export CC=pgcc export CFLAGS='-O2 -fPIC -fastsse -Bstatic' export F77=pgf77 export FFLAGS='-O2 -fPIC -fastsse -Bstatic' export FETK_SRC=/home/xqwang/apbs export FETK_PREFIX=/home/xqwang/apbs/soft export FETK_INCLUDE=${FETK_PREFIX}/include export FETK_LIBRARY=${FETK_PREFIX}/lib export FETK_MPI_INCLUDE=/usr/local/mpich_pg/include export FETK_MPI_LIBRARY=/usr/local/mpich_pg/lib compiling MALOC ./configure --prefix=${FETK_PREFIX} --enable-mpi --disable-blas make make install compiling APBS ./configure --prefix=${FETK_PREFIX} --with-blas="-L/usr/lib64 -lblas" make ------------------------------------------------------------------------ I compiled APBS/MALOC on p4 single cpu and found that file "apbslibc.so" was created in apbs-0.3.2/tools/python/. When I compile APBS on AMD64 cluster, it cannot create "apbslibc.so". But I find that "apbs" has been created in apbs-0.3.2/bin/,so I ignore the error and run "make install". Maybe there are some files in /tools cannot be used. Is it affects the running of "apbs"? Sincerely, Xiaoqing > This is a strange error -- I don't know why the code was being compiled into > shared libraries. Can you send me the environmental variables and configure > command you used? > > Thanks, > > Nathan > > --- Xiaoqing Wang <kit...@12...> wrote: > > > Hi, > > I compile APBS following the "Source installation" section of > > user-guide on amd64 cluster. > > The "make" error as follows > > -------------------------------------------------------- > > pgf77 -O2 -fPIC -fastsse -Bstatic -o apbslibc.so -shared apbslib.o > > ../../bin/.libs/libapbsmainroutines.a > > ../../src/aaa_lib/.libs/libapbs.a > > -L/home/xqwang/apbs/apbs-0.3.2/lib > > -L/home/xqwang/apbs/soft/lib/x86_64-unknown-linux -lmaloc -L/usr/lib64 > > -lblas -L/usr/local/mpich_pg/lib -lmpich -lm -lreadline > > -lncurses > > > > /usr/bin/ld: /usr/local/mpich_pg/lib/libmpich.a(isend.o): relocation > > R_X86_64_32 can not be used when making a shared object; recompile with > > -fPIC > > /usr/local/mpich_pg/lib/libmpich.a: could not read symbols: Bad value > > make[2]: *** [apbslibc.so] Error 2 > > make[2]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools/python' > > make[1]: *** [all-recursive] Error 1 > > make[1]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools' > > ------------------------------------------------------------------ > > > > I run "./configure --help" and find that optional features > > "--enable-static=PKGS build static libraries default=yes". Why it makes > > shared object? > > > > How can I solve this problem? > > > > Any tips would be greatly appreciated! > > > > Sincerely, > > Xiaoqing > > > > > > _______________________________________________ > > apbs-users mailing list > > apb...@ch... > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > > > > > -- > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > Washington University in St. Louis > http://cholla.wustl.edu -- --Xiaoqing Wuhan University Wuhan 430072 China |
From: Xiaoqing W. <kit...@12...> - 2005-06-17 05:11:25
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Hi, The environmental variables and configure commands as follows: ----------------------------------------------------------------- export CC=pgcc export CFLAGS='-O2 -fPIC -fastsse -Bstatic' export F77=pgf77 export FFLAGS='-O2 -fPIC -fastsse -Bstatic' export FETK_SRC=/home/xqwang/apbs export FETK_PREFIX=/home/xqwang/apbs/soft export FETK_INCLUDE=${FETK_PREFIX}/include export FETK_LIBRARY=${FETK_PREFIX}/lib export FETK_MPI_INCLUDE=/usr/local/mpich_pg/include export FETK_MPI_LIBRARY=/usr/local/mpich_pg/lib compiling MALOC ./configure --prefix=${FETK_PREFIX} --enable-mpi --disable-blas make make install compiling APBS ./configure --prefix=${FETK_PREFIX} --with-blas="-L/usr/lib64 -lblas" make ------------------------------------------------------------------------ I compiled APBS/MALOC on p4 single cpu and found that file "apbslibc.so" was created in apbs-0.3.2/tools/python/. When I compile APBS on AMD64 cluster, it cannot create "apbslibc.so". But I find that "apbs" has been created in apbs-0.3.2/bin/,so I ignore the error and run "make install". Maybe there are some files in /tools cannot be used. Is it affects the running of "apbs"? Sincerely, Xiaoqing > This is a strange error -- I don't know why the code was being compiled into > shared libraries. Can you send me the environmental variables and configure > command you used? > > Thanks, > > Nathan > > --- Xiaoqing Wang <kit...@12...> wrote: > > > Hi, > > I compile APBS following the "Source installation" section of > > user-guide on amd64 cluster. > > The "make" error as follows > > -------------------------------------------------------- > > pgf77 -O2 -fPIC -fastsse -Bstatic -o apbslibc.so -shared apbslib.o > > ../../bin/.libs/libapbsmainroutines.a > > ../../src/aaa_lib/.libs/libapbs.a > > -L/home/xqwang/apbs/apbs-0.3.2/lib > > -L/home/xqwang/apbs/soft/lib/x86_64-unknown-linux -lmaloc -L/usr/lib64 > > -lblas -L/usr/local/mpich_pg/lib -lmpich -lm -lreadline > > -lncurses > > > > /usr/bin/ld: /usr/local/mpich_pg/lib/libmpich.a(isend.o): relocation > > R_X86_64_32 can not be used when making a shared object; recompile with > > -fPIC > > /usr/local/mpich_pg/lib/libmpich.a: could not read symbols: Bad value > > make[2]: *** [apbslibc.so] Error 2 > > make[2]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools/python' > > make[1]: *** [all-recursive] Error 1 > > make[1]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools' > > ------------------------------------------------------------------ > > > > I run "./configure --help" and find that optional features > > "--enable-static=PKGS build static libraries default=yes". Why it makes > > shared object? > > > > How can I solve this problem? > > > > Any tips would be greatly appreciated! > > > > Sincerely, > > Xiaoqing > > > > > > _______________________________________________ > > apbs-users mailing list > > apb...@ch... > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > > > > > -- > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > Washington University in St. Louis > http://cholla.wustl.edu |
From: Xiaoqing W. <kit...@12...> - 2005-06-19 14:59:34
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Hi, I run the parallel apbs which I have compiled on AMD64 cluster with input file apbs-PARALLEL.in (apbs-0.3.2/examples/actin-dimer/). But there are only some of the processors write potential, e.g. only pot-PE1.dx pot-PE2.dx pot-PE5.dx and pot-PE6.dx are created. The "io.mc" files of other processors ended with: ------------------------------------------------------------ fillcoCharge: Calling fillcoChargeSpline1... Vpmg_fillco: filling in source term. Vpmg_fillco: marking ion and solvent accessibility. fillcoCoef: Calling fillcoCoefMol... Vpmg_fillco: filling coefficient arrays -------------------------------------------------------------- How I can check this problem? Any tips would be greatly appreciated! Sincerely, Xiaoqing > The environmental variables and configure commands as follows: > ----------------------------------------------------------------- > export CC=pgcc > export CFLAGS='-O2 -fPIC -fastsse -Bstatic' > export F77=pgf77 > export FFLAGS='-O2 -fPIC -fastsse -Bstatic' > > export FETK_SRC=/home/xqwang/apbs > export FETK_PREFIX=/home/xqwang/apbs/soft > export FETK_INCLUDE=${FETK_PREFIX}/include > export FETK_LIBRARY=${FETK_PREFIX}/lib > > export FETK_MPI_INCLUDE=/usr/local/mpich_pg/include > export FETK_MPI_LIBRARY=/usr/local/mpich_pg/lib > > compiling MALOC > ./configure --prefix=${FETK_PREFIX} --enable-mpi --disable-blas > make > make install > > compiling APBS > ./configure --prefix=${FETK_PREFIX} --with-blas="-L/usr/lib64 -lblas" > make > ------------------------------------------------------------------------ > > I compiled APBS/MALOC on p4 single cpu and found that file "apbslibc.so" > was created in apbs-0.3.2/tools/python/. > > When I compile APBS on AMD64 cluster, it cannot create "apbslibc.so". > But I find that "apbs" has been created in apbs-0.3.2/bin/,so I ignore > the error and run "make install". > Maybe there are some files in /tools cannot be used. Is it affects the > running of "apbs"? > > Sincerely, > Xiaoqing > > > This is a strange error -- I don't know why the code was being compiled into > > shared libraries. Can you send me the environmental variables and configure > > command you used? > > > > Thanks, > > > > Nathan > > > > --- Xiaoqing Wang <kit...@12...> wrote: > > > > > Hi, > > > I compile APBS following the "Source installation" section of > > > user-guide on amd64 cluster. > > > The "make" error as follows > > > -------------------------------------------------------- > > > pgf77 -O2 -fPIC -fastsse -Bstatic -o apbslibc.so -shared apbslib.o > > > ../../bin/.libs/libapbsmainroutines.a > > > ../../src/aaa_lib/.libs/libapbs.a > > > -L/home/xqwang/apbs/apbs-0.3.2/lib > > > -L/home/xqwang/apbs/soft/lib/x86_64-unknown-linux -lmaloc -L/usr/lib64 > > > -lblas -L/usr/local/mpich_pg/lib -lmpich -lm -lreadline > > > -lncurses > > > > > > /usr/bin/ld: /usr/local/mpich_pg/lib/libmpich.a(isend.o): relocation > > > R_X86_64_32 can not be used when making a shared object; recompile with > > > -fPIC > > > /usr/local/mpich_pg/lib/libmpich.a: could not read symbols: Bad value > > > make[2]: *** [apbslibc.so] Error 2 > > > make[2]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools/python' > > > make[1]: *** [all-recursive] Error 1 > > > make[1]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools' > > > ------------------------------------------------------------------ > > > > > > I run "./configure --help" and find that optional features > > > "--enable-static=PKGS build static libraries default=yes". Why it makes > > > shared object? > > > > > > How can I solve this problem? > > > > > > Any tips would be greatly appreciated! > > > > > > Sincerely, > > > Xiaoqing > > > > > > > > > _______________________________________________ > > > apbs-users mailing list > > > apb...@ch... > > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > > > > > > > > > > -- > > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > > Washington University in St. Louis > > http://cholla.wustl.edu > > > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users -- --Xiaoqing Wuhan University Wuhan 430072 China |
From: Nathan B. <sob...@ya...> - 2005-06-20 13:21:35
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Hello -- My comments are below... > I run the parallel apbs which I have compiled on AMD64 cluster with > input file apbs-PARALLEL.in (apbs-0.3.2/examples/actin-dimer/). > But there are only some of the processors write potential, e.g. only > pot-PE1.dx pot-PE2.dx pot-PE5.dx and pot-PE6.dx are created. This often happens due to memory limitations on the individual processors. Did you monitor memory usage during the run -- e.g. using top or something similar? > The "io.mc" files of other processors ended with: > ------------------------------------------------------------ > fillcoCharge: Calling fillcoChargeSpline1... > Vpmg_fillco: filling in source term. > Vpmg_fillco: marking ion and solvent accessibility. > fillcoCoef: Calling fillcoCoefMol... > Vpmg_fillco: filling coefficient arrays > -------------------------------------------------------------- Did any solver-related messages (iterations, etc.) appear prior to these? In other words, I'd like to determine if the run died during setup or later. > How I can check this problem? > Any tips would be greatly appreciated! > > Sincerely, > Xiaoqing > > > The environmental variables and configure commands as follows: > > ----------------------------------------------------------------- > > export CC=pgcc > > export CFLAGS='-O2 -fPIC -fastsse -Bstatic' > > export F77=pgf77 > > export FFLAGS='-O2 -fPIC -fastsse -Bstatic' > > > > export FETK_SRC=/home/xqwang/apbs > > export FETK_PREFIX=/home/xqwang/apbs/soft > > export FETK_INCLUDE=${FETK_PREFIX}/include > > export FETK_LIBRARY=${FETK_PREFIX}/lib > > > > export FETK_MPI_INCLUDE=/usr/local/mpich_pg/include > > export FETK_MPI_LIBRARY=/usr/local/mpich_pg/lib > > > > compiling MALOC > > ./configure --prefix=${FETK_PREFIX} --enable-mpi --disable-blas > > make > > make install > > > > compiling APBS > > ./configure --prefix=${FETK_PREFIX} --with-blas="-L/usr/lib64 -lblas" > > make > > ------------------------------------------------------------------------ > > > > I compiled APBS/MALOC on p4 single cpu and found that file "apbslibc.so" > > was created in apbs-0.3.2/tools/python/. > > > > When I compile APBS on AMD64 cluster, it cannot create "apbslibc.so". > > But I find that "apbs" has been created in apbs-0.3.2/bin/,so I ignore > > the error and run "make install". > > Maybe there are some files in /tools cannot be used. Is it affects the > > running of "apbs"? > > > > Sincerely, > > Xiaoqing > > > > > This is a strange error -- I don't know why the code was being compiled > into > > > shared libraries. Can you send me the environmental variables and > configure > > > command you used? > > > > > > Thanks, > > > > > > Nathan > > > > > > --- Xiaoqing Wang <kit...@12...> wrote: > > > > > > > Hi, > > > > I compile APBS following the "Source installation" section of > > > > user-guide on amd64 cluster. > > > > The "make" error as follows > > > > -------------------------------------------------------- > > > > pgf77 -O2 -fPIC -fastsse -Bstatic -o apbslibc.so -shared apbslib.o > > > > ../../bin/.libs/libapbsmainroutines.a > > > > ../../src/aaa_lib/.libs/libapbs.a > > > > -L/home/xqwang/apbs/apbs-0.3.2/lib > > > > -L/home/xqwang/apbs/soft/lib/x86_64-unknown-linux -lmaloc -L/usr/lib64 > > > > -lblas -L/usr/local/mpich_pg/lib -lmpich -lm -lreadline > > > > -lncurses > > > > > > > > > /usr/bin/ld: /usr/local/mpich_pg/lib/libmpich.a(isend.o): relocation > > > > R_X86_64_32 can not be used when making a shared object; recompile with > > > > -fPIC > > > > /usr/local/mpich_pg/lib/libmpich.a: could not read symbols: Bad value > > > > make[2]: *** [apbslibc.so] Error 2 > > > > make[2]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools/python' > > > > make[1]: *** [all-recursive] Error 1 > > > > make[1]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools' > > > > ------------------------------------------------------------------ > > > > > > > > I run "./configure --help" and find that optional features > > > > "--enable-static=PKGS build static libraries default=yes". Why it > makes > > > > shared object? > > > > > > > > How can I solve this problem? > > > > > > > > Any tips would be greatly appreciated! > > > > > > > > Sincerely, > > > > Xiaoqing > > > > > > > > > > > > _______________________________________________ > > > > apbs-users mailing list > > > > apb...@ch... > > > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > > > > > > > > > > > > > > > -- > > > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > > > Washington University in St. Louis > > > http://cholla.wustl.edu > > > > > > > > _______________________________________________ > > apbs-users mailing list > > apb...@ch... > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > -- > --Xiaoqing > Wuhan University > Wuhan 430072 > China > > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu |
From: Nathan B. <sob...@ya...> - 2005-06-20 13:43:46
|
Hello -- > I compiled APBS/MALOC on p4 single cpu and found that file "apbslibc.so" > was created in apbs-0.3.2/tools/python/. This is used for Python code and is not absolutely necessary. > When I compile APBS on AMD64 cluster, it cannot create "apbslibc.so". > But I find that "apbs" has been created in apbs-0.3.2/bin/,so I ignore > the error and run "make install". That's fine... > Maybe there are some files in /tools cannot be used. Is it affects the > running of "apbs"? No, you should be OK -- the shared library is only used for Python development and not by the main APBS executable. Thanks, Nathan > > > This is a strange error -- I don't know why the code was being compiled > into > > shared libraries. Can you send me the environmental variables and > configure > > command you used? > > > > Thanks, > > > > Nathan > > > > --- Xiaoqing Wang <kit...@12...> wrote: > > > > > Hi, > > > I compile APBS following the "Source installation" section of > > > user-guide on amd64 cluster. > > > The "make" error as follows > > > -------------------------------------------------------- > > > pgf77 -O2 -fPIC -fastsse -Bstatic -o apbslibc.so -shared apbslib.o > > > ../../bin/.libs/libapbsmainroutines.a > > > ../../src/aaa_lib/.libs/libapbs.a > > > -L/home/xqwang/apbs/apbs-0.3.2/lib > > > -L/home/xqwang/apbs/soft/lib/x86_64-unknown-linux -lmaloc -L/usr/lib64 > > > -lblas -L/usr/local/mpich_pg/lib -lmpich -lm -lreadline > > > -lncurses > > > > > > > /usr/bin/ld: /usr/local/mpich_pg/lib/libmpich.a(isend.o): relocation > > > R_X86_64_32 can not be used when making a shared object; recompile with > > > -fPIC > > > /usr/local/mpich_pg/lib/libmpich.a: could not read symbols: Bad value > > > make[2]: *** [apbslibc.so] Error 2 > > > make[2]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools/python' > > > make[1]: *** [all-recursive] Error 1 > > > make[1]: Leaving directory `/home/xqwang/apbs/apbs-0.3.2/tools' > > > ------------------------------------------------------------------ > > > > > > I run "./configure --help" and find that optional features > > > "--enable-static=PKGS build static libraries default=yes". Why it makes > > > shared object? > > > > > > How can I solve this problem? > > > > > > Any tips would be greatly appreciated! > > > > > > Sincerely, > > > Xiaoqing > > > > > > > > > _______________________________________________ > > > apbs-users mailing list > > > apb...@ch... > > > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > > > > > > > > > > > -- > > Assistant Professor, Dept. of Biochemistry and Molecular Biophysics > > Washington University in St. Louis > > http://cholla.wustl.edu > > > > _______________________________________________ > apbs-users mailing list > apb...@ch... > http://cholla.wustl.edu/mailman/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Washington University in St. Louis http://cholla.wustl.edu |