Laura, If you want to build the Parallel HDF5, you need to --enable-parallel. You need to disable optimization with --disable-production. So your command becomes like this:
CC=/usr/local/mpich2-1.4.1p1-gfortran/bin/mpicc \ sudo ./configure --disable-production --enable-parallel --prefix=/usr/local/hdf5-1.8.9-gfortran --with-zlib=/usr/local/zlib-1.2.7-gfortran If you don't need Parallel HDF5, your command is like this: sudo ./configure --disable-production --prefix=/usr/local/hdf5-1.8.9-gfortran --with-zlib=/usr/local/zlib-1.2.7-gfortran I hope it helps. Ray On Jun 27, 2012, at 6:22 PM, ldfowler wrote: > Hi Ray: > Thanks for replying to my e-mail. I tried to rerun ./configure without > optimization for gcc. I did > > CC=/usr/local/mpich2-1.4.1p1-gfortran/bin/mpicc > CFLAGS=-O0 > sudo ./configure --prefix=/usr/local/hdf5-1.8.9-gfortran > --with-zlib=/usr/local/zlib-1.2.7-gfortran > > then > sudo make > sudo make check > > I bumped into the same error. Is it the correct way to remove the > optimization when using gcc? > > Also, if I want to use the hdf5 libraries do I need to add --enable-fortran > with my ./configure? In that case, do I need to set FC=mpif90? What about > CFLAGS? Finally, at the bottom of my configure output I have > > Features: > --------- > Parallel HDF5: no > High Level library: yes > Threadsafety: no > Default API Mapping: v18 > With Deprecated Public Symbols: yes > I/O filters (external): deflate(zlib) > I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset > MPE: no > Direct VFD: no > dmalloc: no > Clear file buffers before write: yes > Using memory checker: no > Function Stack Tracing: no > GPFS: no > Strict File Format Checks: no > Optimization Instrumentation: no > Large File Support (LFS): yes > > Do I need to also use --enable-parallel? Thanks, > > Laura > > > > > > On Jun 27, 2012, at 9:31 AM, Raymond Lu wrote: > >> Laura, >> >> We're aware that the default GCC (4.2.1) on Mac Lion has problem with the >> data conversion test dt_arith.c from "long double" to other datatypes. It >> only happens with optimization (-O1, -O2, and -O3). Some newer versions of >> GCC do not have this problem. You can either disable optimization or try >> new version of GCC. Please let us know whether you're able to work around >> it. >> >> Thanks. >> >> Ray >> >> On Jun 22, 2012, at 3:49 PM, ldfowler wrote: >> >>> Hi: >>> I am trying to install parallel hdf5-1.8.9 on my MacBookPro which runs OSX >>> 10.7.4. I am using gfortran and gcc that I downloaded from >>> http://hpc.sourceforge.net/. See info below gfortran and gcc. >>> >>> cloudbug-2:Downloads LAURA$ gfortran -v >>> Using built-in specs. >>> COLLECT_GCC=gfortran >>> COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin11.4.0/4.8.0/lto-wrapper >>> Target: x86_64-apple-darwin11.4.0 >>> Configured with: ../gcc-4.8-20120603/configure --enable-languages=fortran >>> Thread model: posix >>> gcc version 4.8.0 20120603 (experimental) (GCC) >>> >>> cloudbug-2:Downloads LAURA$ gcc -v >>> Using built-in specs. >>> Target: i686-apple-darwin11 >>> Configured with: >>> /private/var/tmp/llvmgcc42/llvmgcc42-2336.9~22/src/configure >>> --disable-checking --enable-werror >>> --prefix=/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2 >>> --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ >>> --program-prefix=llvm- --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ >>> --with-slibdir=/usr/lib --build=i686-apple-darwin11 >>> --enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2336.9~22/dst-llvmCore/Developer/usr/local >>> --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11 >>> --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1 >>> Thread model: posix >>> gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.9.00) >>> >>> I define CC=mpicc, and then ran ./configure. When I do make check, I get >>> the following error messages: >>> >>> Testing hard normalized double -> long conversions >>> PASSED >>> Testing hard normalized float -> unsigned long conversions >>> PASSED >>> Testing hard normalized double -> unsigned long conversions >>> PASSED >>> Testing hard normalized long double -> signed char conversions >>> Command terminated abnormally. >>> 1.72 real 0.10 user 0.02 sys >>> make[4]: *** [dt_arith.chkexe_] Error 1 >>> make[3]: *** [build-check-s] Error 2 >>> make[2]: *** [test] Error 2 >>> make[1]: *** [check-am] Error 2 >>> make: *** [check-recursive] Error 1 >>> cloudbug-2:hdf5-1.8.9 LAURA$ cd >>> >>> and >>> >>> Testing hard special double -> long double conversions >>> PASSED >>> Testing hard special long double -> float conversions >>> Child caught signal 11. >>> Testing hard special long double -> double conversions >>> Child caught signal 11. >>> Testing hard signed char -> unsigned char conversions >>> PASSED >>> >>> Can somebody help me figure out how to debug this issue. >>> >>> Thanks, >>> Laura >>> >>> !===================================================== >>> ! Laura D. Fowler >>> ! e-mail: [email protected] >>> ! Phone: 970-215-0516 >>> !===================================================== >>> >>> >>> _______________________________________________ >>> Hdf-forum is for HDF software users discussion. >>> [email protected] >>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >> >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
