I'm trying to install netcdf (pgi vervion) in the Ubuntu-12.04 with gcc-4.6. However, when I configure ./configure FC=pgf90 CC=gcc CXX=g++ --prefix=$HOME/netcdf-pgi, the errors show this:
configure:3986: $? = 0
configure:3993: gcc -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
configure:3997: $? = 0
configure:4004: gcc -V >&5
gcc: error: unrecognized option '-V'
gcc: fatal error: no input files
compilation terminated.
If you want to compile netcdf with the PGI (Portland group) compilers, then you should use those tools:
PGF77 , PGFORTRAN , PGC++ and PGCC
In this link is a guide to build and install it correctly. Portland Group NETCDF 4.11 Build guide
Related
I am trying to set up the environment variables to add additional search paths for my gcc compilation. However, for some reason these are not working. What am I missing?
$ CPATH=/usr/local/boost/include
$ echo $CPATH
/usr/local/boost/include
$ cpp -v
Using built-in specs.
COLLECT_GCC=cpp
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.4' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4)
COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'
/usr/lib/gcc/x86_64-linux-gnu/5/cc1 -E -quiet -v -imultiarch x86_64-linux-gnu - -mtune=generic -march=x86-64 -fstack-protector-strong -Wformat -Wformat-security
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/5/../../../../x86_64-linux-gnu/include"
#include "..." search starts here:
#include <...> search starts here:
/usr/lib/gcc/x86_64-linux-gnu/5/include
/usr/local/include
/usr/lib/gcc/x86_64-linux-gnu/5/include-fixed
/usr/include/x86_64-linux-gnu
/usr/include
End of search list.
As you can see, in the "#include search starts here:" the path specified via CPATH does not exist. I tried the same with C_INCLUDE_PATH and CPLUS_INCLUDE_PATH.
Also, the problem appeared when actually trying to compile a cpp file using g++, but in the listing above I just use cpp -v for the sake of brevity.
The specified path does exist in the file system.
Any additional information you might need?
When I use -fsanitize=address to link some object into a binary, g++ says the two lib in the title do not exist.
My g++ version is:
$ /opt/rh/devtoolset-2/root/usr/bin/g++ -v
Using built-in specs.
COLLECT_GCC=/opt/rh/devtoolset-2/root/usr/bin/g++
COLLECT_LTO_WRAPPER=/opt/rh/devtoolset-2/root/usr/libexec/gcc/x86_64-redhat-linux/4.8.2/lto-wrapper
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/opt/rh/devtoolset-2/root/usr --mandir=/opt/rh/devtoolset-2/root/usr/share/man --infodir=/opt/rh/devtoolset-2/root/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --enable-languages=c,c++,fortran,lto --enable-plugin --with-linker-hash-style=gnu --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.2-20140120/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.2-20140120/obj-x86_64-redhat-linux/cloog-install --with-mpc=/builddir/build/BUILD/gcc-4.8.2-20140120/obj-x86_64-redhat-linux/mpc-install --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.8.2 20140120 (Red Hat 4.8.2-15) (GCC)
Do I need to manually compile libasan if I use g++?
Sanitizer runtimes typically come in a separate package. E.g. on Debian you'll need to install libasanN ("N" depends on your GCC version).
I can not compile a simple c program without specifying '-march=native', I need to run it as: 'gcc -march=native -o hello hello.c'.
I did:
export CFLAGS='-march=native'
export CXXFLAGS='-march=native'
but didn't help.
user#server:~$ gcc -march=native -Q --help=target
...
-march=corei7-avx
...
Output of gcc -v:
user#server:~$ gcc -v
Using built-in specs.
gcc: error: missing argument to ‘-march=’
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.7/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Debian 4.7.2-5' --with-bugurl=file:///usr/share/doc/gcc-4.7/README.Bugs --enable-languages=c,c++,go,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.7 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.7 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --with-arch-32=i586 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.7.2 (Debian 4.7.2-5)
Where and how can I add this option to be default?
Two options:
Hard way. You may dump your specs file with gcc -dumpspecs > specs
command. Now put this file to /usr/lib/gcc/x86_64-linux-gnu/4.7/
folder and edit it to add option as described in documentation.
In your case I suggest to start from removing all
march=<something> lines, this might trivially help. But general case is troubles and creativity at this point.
Easy way: rename gcc binary to, say gcc-4.7 and make alias with
alias gcc='gcc-4.7 -march=native'
I have gcc installed, however as (the assembler) is not working correctly. I get the following error
gcc tmp.c
fatal error: as: unknown host architecture (can't determine which assembler to run)
I get the same error when I run as. I think its something to do with the configuration of gcc, but I am not certain. (My cpu is an intel core 2, so the --with-arch32=i686 might be an issue)
Some possible useful information
$ gcc -dumpmachine
x86_64-linux-gnu
$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.8.1-10ubuntu9' `--with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu`
Thread model: posix
gcc version 4.8.1 (Ubuntu/Linaro 4.8.1-10ubuntu9)
$ uname -mpio
x86_64 x86_64 x86_64 GNU/Linux
Any help would be greatly apprectiated. :)
I'm building a DSO under 32-bit GCC 4.2.5 and 64-bit GCC. The 64-bit DSO has extra entries in the dynamic symbol table (nm -D libname.so) that don't appear in the 32-bit DSO.
I'm almost positive this is because the 32-bit DSO uses a static version of libstdc++: all of the extra entries in the table are related to std::vector. Some examples:
W _ZNSt6vectorIPN3BVT17FileSonarListenerESaIS2_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS2_S4_EERKS2_
W _ZNSt6vectorIPN3BVT3Net16UDPMessageSocketESaIS3_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS3_S5_EERKS3_
W _ZNSt6vectorIPN3BVT3Net21MessageSocketListenerESaIS3_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS3_S5_EERKS3_
W _ZNSt6vectorIPN3BVT4HeadESaIS2_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS2_S4_EERKS2_
W _ZSt6__findIN9__gnu_cxx17__normal_iteratorIPN3BVT15ServerDiscovery5EntryESt6vectorIS4_SaIS4_EEEES4_ET_SA_SA_RKT0_St26random_access_iterator_tag
The other symbols in the table are explicitly flagged in the source with default visibility with a traditional DLL_EXPORT macro, and I'm compiling with the -fvisibility=hidden flag.
Is there any way to remove these unexpected symbols without affecting clients of the DSO? The DSO defines a pure C interface, so no STL types are being passed around.
Here is the output of gcc -v for both compilers:
Configured with: ../src/configure -v
--enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr
--enable-shared --with-system-zlib --libexecdir=/usr/lib
--without-included-gettext --enable-threads=posix --enable-nls
--with-gxx-include-dir=/usr/include/c++/4.2 --program-suffix=-4.2
--enable-clocale=gnu --enable-libstdcxx-debug --enable-objc-gc
--enable-mpfr --enable-targets=all --enable-checking=release
--build=i486-linux-gnu --host=i486-linux-gnu --target=i486-linux-gnu
Thread model: posix gcc version 4.2.4 (Ubuntu 4.2.4-1ubuntu4)
Target: x86_64-linux-gnu
Configured with: ../src/configure -v
--with-pkgversion='Ubuntu/Linaro 4.5.2-8ubuntu4'
--with-bugurl=file:///usr/share/doc/gcc-4.5/README.Bugs
--enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
--program-suffix=-4.5 --enable-shared --enable-multiarch
--with-multiarch-defaults=x86_64-linux-gnu --enable-linker-build-id
--with-system-zlib --libexecdir=/usr/lib/x86_64-linux-gnu
--without-included-gettext --enable-threads=posix
--with-gxx-include-dir=/usr/include/c++/4.5
--libdir=/usr/lib/x86_64-linux-gnu --enable-nls --with-sysroot=/
--enable-clocale=gnu --enable-libstdcxx-debug
--enable-libstdcxx-time=yes --enable-plugin --enable-gold
--enable-ld=default --with-plugin-ld=ld.gold --enable-objc-gc
--disable-werror --with-arch-32=i686 --with-tune=generic
--enable-checking=release --build=x86_64-linux-gnu
--host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix
gcc version 4.5.2 (Ubuntu/Linaro 4.5.2-8ubuntu4)
Perhaps you could link -lstdc++ when building your .so files? Something like g++ -shared -o yourlib.so yourobjects*.pic.o -lstdc++
And perhaps using a more recent GCC (e.g. 4.6) could help.