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: ldfowler58@me.com
! Phone: 970-215-0516
!=====================================================
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: ldfowler58@me.com
! Phone: 970-215-0516
!=====================================================
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
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: ldfowler58@me.com
! Phone: 970-215-0516
!=====================================================
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
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: ldfowler58@me.com
! Phone: 970-215-0516
!=====================================================
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Laura,
I forgot to mention Fortran. Yes, you'll need to --enable-fortran. To specify a Fortran compiler, set FC variable. You can do ./configure --help to list all commands and variables. So your command will become like this:
CC=/usr/local/mpich2-1.4.1p1-gfortran/bin/mpicc \
FC=mpif90 \
sudo ./configure --disable-production --enable-parallel --enable-fortran --prefix=/usr/local/hdf5-1.8.9-gfortran --with-zlib=/usr/local/zlib-1.2.7-gfortran
The Fortran compiler flags go with the FCFLAGS.
Ray
···
On Jun 28, 2012, at 10:35 AM, Raymond Lu wrote:
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: ldfowler58@me.com
! Phone: 970-215-0516
!=====================================================
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
