gcc and gfortran
hi dear
how and where can i determine cc and fc compilers in my system (fedora 16)? i know that my system has those compilers but i think that their paths have not been defined for system because i check env file in etc/bin/ and dont see CC=gcc FC=gfortran in env file. please tell me how i can set them? thanks |
CC = gcc : CC is always /usr/bin/gcc(-4.6.x), unless you specify different.
FC : The various fortran's are checked. If you have gfortran only, /usr/bin/gfortran(-4.6.x) will be used. Unless the program to compile specifically requires pgf90, ifort, "old g77 / f77", etc. There is no such thing as setting a PATH for the "4000" default executable'. But : Your PATH / the system PATH is set to /bin:/usr/bin:/usr/local/bin: ? :? → → Please try out the command $ env | grep PATH ... to know the default system settings. Installing the Fedora compilers : # yum install gcc-c++ gfortran compat-gcc-34-c++ compat-gcc-g77 Setting a different compiler, examples : gcc34 file.c ; g++34 file.cpp ; g77 file.f ; export CC=gcc34 CXX=g++34 && ./configure - |
but be warned
Fedora 16 is past it's end of life the mirrors will be disappearing Fedora 16 and 17 are no longer supported only fedora 18 and 19 are also of note g77 and gfortran are not the same the old g77 is deprecated , but around for all the old code that is still usable and a lot of it is still being used |
gcc and g fortran
dear
i check my labtop defaul paths. i set up my labtop like pc system. in ps system i see cc=gcc and fc=gfortran but in labtop those mention paths dont exist. see below: [fereshteh@localhost ~]$ env XDG_VTNR=1 MKLROOT=/opt/intel/Compiler/11.1/080/mkl MANPATH=/opt/intel/Compiler/11.1/080/man/en_US:/opt/intel/Compiler/11.1/080/mkl/man/en_US:/opt/intel/Compiler/11.1/080/mkl/../man/en_US:/opt/intel/Compiler/11.1/080/man/en_US:/opt/intel/Compiler/11.1/080/mkl/man/en_US:/opt/intel/Compiler/11.1/080/mkl/../man/en_US:/opt/intel/Compiler/11.1/080/man/en_US:/opt/intel/Compiler/11.1/080/mkl/man/en_US:/opt/intel/Compiler/11.1/080/mkl/../man/en_US:/opt/intel/Compiler/11.1/080/man/en_US:/opt/intel/Compiler/11.1/080/mkl/man/en_US:/opt/intel/Compiler/11.1/080/mkl/../man/en_US:/usr/local/share/man:/usr/share/man XDG_SESSION_ID=2 LC_MONETARY=en_US.utf8 HOSTNAME=localhost.localdomain IMSETTINGS_INTEGRATE_DESKTOP=yes GPG_AGENT_INFO=/tmp/keyring-uq51Rs/gpg:0:1 IPPROOT=/opt/intel/Compiler/11.1/080/ipp/ia32 INTEL_LICENSE_FILE=/opt/intel/Compiler/11.1/080/licenses:/opt/intel/licenses:/home/fereshteh/intel/licenses:/opt/intel/Compiler/11.1/080/licenses:/opt/intel/licenses:/home/fereshteh/intel/licenses:/opt/intel/Compiler/11.1/080/licenses:/opt/intel/licenses:/home/fereshteh/intel/licenses:/opt/intel/Compiler/11.1/080/licenses:/opt/intel/licenses:/home/fereshteh/intel/licenses TERM=xterm SHELL=/bin/bash XDG_SESSION_COOKIE=040bd5238ad97d2d598bb0f300000018-1373809743.353869-2016389964 HISTSIZE=1000 LIBRARY_PATH=/opt/intel/Compiler/11.1/080/lib/ia32:/opt/intel/Compiler/11.1/080/ipp/ia32/lib:/opt/intel/Compiler/11.1/080/mkl/lib/32:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.1/080/lib/ia32:/opt/intel/Compiler/11.1/080/ipp/ia32/lib:/opt/intel/Compiler/11.1/080/mkl/lib/32:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.1/080/lib/ia32:/opt/intel/Compiler/11.1/080/ipp/ia32/lib:/opt/intel/Compiler/11.1/080/mkl/lib/32:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.1/080/lib/ia32:/opt/intel/Compiler/11.1/080/ipp/ia32/lib:/opt/intel/Compiler/11.1/080/mkl/lib/32:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib GJS_DEBUG_OUTPUT=stderr WINDOWID=33554437 LC_NUMERIC=en_US.utf8 FPATH=/opt/intel/Compiler/11.1/080/mkl/include:/opt/intel/Compiler/11.1/080/mkl/include:/opt/intel/Compiler/11.1/080/mkl/include:/opt/intel/Compiler/11.1/080/mkl/include GNOME_KEYRING_CONTROL=/tmp/keyring-uq51Rs GJS_DEBUG_TOPICS=JS ERROR;JS LOG IMSETTINGS_MODULE=none USER=fereshteh LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;0 1:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01 ;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.zip=01;31:*.z=01;31:* .Z=01;31:*.dz=01;31:*.gz=01;31:*.lz=01;31:*.xz=01;31:*.bz2=01;31:*.tbz=01;31:*.tbz2=01;31:*.bz=01;31 :*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.ac e=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01 ;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35 :*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:* .m2v=01;35:*.mkv=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv =01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01; 35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.a nx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka= 01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36 :*.xspf=01;36:*.pdf=00;33:*.ps=00;33:*.ps.gz=00;33:*.txt=00;33:*.patch=00;33:*.diff=00;33:*.log=00;3 3:*.tex=00;33:*.xls=00;33:*.xlsx=00;33:*.ppt=00;33:*.pptx=00;33:*.rtf=00;33:*.doc=00;33:*.docx=00;33 :*.odt=00;33:*.ods=00;33:*.odp=00;33:*.xml=00;33:*.epub=00;33:*.abw=00;33:*.html=00;33:*.wpd=00;33: LD_LIBRARY_PATH=/opt/intel/Compiler/11.1/080/lib/ia32:/opt/intel/Compiler/11.1/080/ipp/ia32/sharedlib:/opt/intel/Compiler/11.1/080/mkl/lib/32:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.1/080/lib/ia32:/opt/intel/Compiler/11.1/080/ipp/ia32/sharedlib:/opt/intel/Compiler/11.1/080/mkl/lib/32:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.1/080/lib/ia32:/opt/intel/Compiler/11.1/080/ipp/ia32/sharedlib:/opt/intel/Compiler/11.1/080/mkl/lib/32:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.1/080/lib/ia32:/opt/intel/Compiler/11.1/080/ipp/ia32/sharedlib:/opt/intel/Compiler/11.1/080/mkl/lib/32:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib LIB=/opt/intel/Compiler/11.1/080/ipp/ia32/lib:/opt/intel/Compiler/11.1/080/ipp/ia32/lib:/opt/intel/Compiler/11.1/080/ipp/ia32/lib:/opt/intel/Compiler/11.1/080/ipp/ia32/lib: CPATH=/opt/intel/Compiler/11.1/080/ipp/ia32/include:/opt/intel/Compiler/11.1/080/mkl/include:/opt/intel/Compiler/11.1/080/tbb/include:/opt/intel/Compiler/11.1/080/ipp/ia32/include:/opt/intel/Compiler/11.1/080/mkl/include:/opt/intel/Compiler/11.1/080/tbb/include:/opt/intel/Compiler/11.1/080/ipp/ia32/include:/opt/intel/Compiler/11.1/080/mkl/include:/opt/intel/Compiler/11.1/080/tbb/include:/opt/intel/Compiler/11.1/080/ipp/ia32/include:/opt/intel/Compiler/11.1/080/mkl/include:/opt/intel/Compiler/11.1/080/tbb/include SSH_AUTH_SOCK=/tmp/keyring-uq51Rs/ssh USERNAME=fereshteh SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/1528,unix/unix:/tmp/.ICE-unix/1528 NLSPATH=/opt/intel/Compiler/11.1/080/lib/ia32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/ipp/ia32/lib/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/mkl/lib/32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/idb/ia32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/lib/ia32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/ipp/ia32/lib/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/mkl/lib/32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/idb/ia32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/lib/ia32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/ipp/ia32/lib/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/mkl/lib/32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/idb/ia32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/lib/ia32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/ipp/ia32/lib/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/mkl/lib/32/locale/%l_%t/%N:/opt/intel/Compiler/11.1/080/idb/ia32/locale/%l_%t/%N DESKTOP_SESSION=gnome MAIL=/var/spool/mail/fereshteh PATH=/opt/intel/Compiler/11.1/080/bin/ia32:/opt/intel/Compiler/11.1/080/bin/ia32:/opt/intel/Compiler/11.1/080/bin/ia32:/opt/intel/Compiler/11.1/080/bin/ia32:/usr/lib/ccache:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/fereshteh/.local/bin:/home/fereshteh/bin QT_IM_MODULE=xim PWD=/home/fereshteh XMODIFIERS=@im=none GNOME_KEYRING_PID=1521 LANG=en_US.utf8 KDE_IS_PRELINKED=1 GDM_LANG=en_US.utf8 KDEDIRS=/usr LC_MEASUREMENT=en_US.utf8 GDMSESSION=gnome HISTCONTROL=ignoredups SHLVL=2 HOME=/home/fereshteh XDG_SEAT=seat0 GNOME_DESKTOP_SESSION_ID=this-is-deprecated DYLD_LIBRARY_PATH=/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib:/opt/intel/Compiler/11.1/080/tbb/ia32/cc4.1.0_libc2.4_kernel2.6.16.21/lib LOGNAME=fereshteh CVS_RSH=ssh DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-sYiZouu32t,guid=3376456f542ffae70bbb357e00000033 LESSOPEN=||/usr/bin/lesspipe.sh %s WINDOWPATH=1 XDG_RUNTIME_DIR=/run/user/fereshteh DISPLAY=:0 INCLUDE=/opt/intel/Compiler/11.1/080/ipp/ia32/include:/opt/intel/Compiler/11.1/080/mkl/include:/opt/intel/Compiler/11.1/080/ipp/ia32/include:/opt/intel/Compiler/11.1/080/mkl/include:/opt/intel/Compiler/11.1/080/ipp/ia32/include:/opt/intel/Compiler/11.1/080/mkl/include:/opt/intel/Compiler/11.1/080/ipp/ia32/include:/opt/intel/Compiler/11.1/080/mkl/include LC_TIME=en_US.utf8 XAUTHORITY=/var/run/gdm/auth-for-fereshteh-t1XeY8/database COLORTERM=gnome-terminal _=/usr/local/bin/env there are not compilers as gcc and gfortran there are intel compiler that i install separatly. when i type [fereshteh@localhost ~]$ gcc --version gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) therefore my system has gcc as default compiler. in my pc system i have cc=gcc anf fc=gfortran by default in env. |
fedora like rhel uses "links" in /usr/bin
and uses GFortran , part of the gcc compiler in my case i have a few versions of the gcc group installed gcc 3.3 , gcc 4.3 and gcc 4.7 -- i have not yet installed the ancient g77 for some code i use , i recently upgraded my OS and have not gotten to it yet . for one of the "current " newer versions gcc 4.7 "/usr/bin/gfortran-4.7" is a symbolic link to "/usr/bin/gfortran" if you try calling g77 or g95 in your build line you will get an error on fedora ( mind you Fedora 16 is WELL past it's end of life ! And is NOT supported and has not been supported since 2013-02-12 - "Feb. 12 20123") use yum to install gfortran ( the current will be installed by default Code:
su - Code:
gfortran -v please post the build line you are using and where this code is from ( if possible ) and the errors you are getting |
$ gcc --version
gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) Copyright (C) 2011 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. $ gfortran -v sing built-in specs. COLLECT_GCC=gfortran Target: i686-redhat-linux Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/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++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch=i686 --build=i686-redhat-linux Thread model: posix gcc version 4.6.2 20111027 (Red Hat 4.6.2-1) (GCC) [fereshteh@localhost ~]$ gcc --version gcc (GCC) 4.6.2 20111027 (Red Hat 4.6.2-1) Copyright (C) 2011 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. when i try to set up zlib 1.2.7 by: [fereshteh@localhost zlib-1.2.7]$ ./configure --prefix=/home/fereshteh/NETCDF_4.2.1.1 Checking for gcc... Checking for shared library support... No shared library support. Building static library libz.a version 1.2.7 with cc. Checking for off64_t... No. Checking for fseeko... No. Checking for strerror... No. Checking for unistd.h... No. Checking for stdarg.h... No. Checking whether to use vs[n]printf() or s[n]printf()... using s[n]printf(). Checking for snprintf() in stdio.h... No. WARNING: snprintf() not found, falling back to sprintf(). zlib can build but will be open to possible buffer-overflow security vulnerabilities. Checking for return value of sprintf()... No. WARNING: apparently sprintf() does not return a value. zlib can build but will be open to possible string-format security vulnerabilities. Looking for a four-byte integer type... Not found. this error arises in labtop system but when i use this in pc that has same fedora version i did not have error like this. please help me to solve it |
might ask "why ?" are you trying to build zlib ?
libz is installed by default and the devel rpm is in the base fedora repo Code:
yum install zlib-devel -- 32 bit -- zlib-1.2.5-7.fc16.i686.rpm zlib-devel-1.2.5-7.fc16.i686.rpm building zlib 1.2.7 from source will REPLACE the default version that is installed and that the Fedora 16 NEEDS!!! from the error warnings you are missing some basic development source code you might want to install the "development group" Code:
su - |
gcc and gfortran
dear i did both of comment that you say
1-yum install zlib-devel 2-yum grouplist... but again by using ./configure -- prefix=/home/user/netcdf4.2.1 for zlib installation same error has appeared. i need to install zlib by source (not rpm) becuase i need to install netcdf with zlib in same location by ./configure --with-zlib=/home/user/netcdf4.2.1 -- prefix=/home/user/netcdf4.2.1 now what is your recommendation thanks |
seeing as "unistd.h" is in the kernel-devel.rpm
stdarg.h is in the libstdc++ rpm Did you install the software development libraries and tools listed in the output of "grouplist " again WHY do you need a different version of libz than the GCC compiler and autotools and the Operating System will use in the build folder of some program Quote:
if it can not find libz.so.???? add it to the linker line things like that are VERY common with fedora ( even a version that is not supported any longer ) somethings -- like Gcc-- are going to be WAY WAY too new to build a lot of programs without hacking that source code TO build with very new versions of programs http://www.unidata.ucar.edu/software/netcdf netcdf-4.3.0.tar.gz is the current , not the old 4.2.1 4.2.1 is listed in the OLD section on the page http://www.unidata.ucar.edu/download..._2_1/index.jsp netcdf-4.2.1.tar.gz dated July of 2012 from the INSTALL text file Quote:
it is installed in /usr/lib or /usr/lib64 the default location just use "--with-zlib" there is NO NEED to have a different version( than the operating system is using ) in the build folder i just ran Code:
./configure |
quesions
Dear
1- i install software development libraries and tools by typing: [code]yum grouplist yum groupinstall "Development Tools as you tooled. I have several questions that become so appreciate to receiving answer. 2- how can i find version of zlip which is already installed ? 3- you mean that i should make a folder as NETCDF for installing netcdf and then what i should copy/ past in that folder? 4-what is linker line and how i can add it ? 5-after coping what i need for zlib (quesion 3), for installing hdf5, i should dressed NETCDF folder (that i make it) in [code] ./configure –with-zlib=/home/usr/NETCDF –prefix=/home/usr/NETCDF make check install 6- and also for installing netcdf do [code] CPPFLAGS=-I/home/usr/NETCD/ include LDFLAGS=L/home/usr/NETCD /lib ./configure –prefix=/home/usr/NETCD4 make check install Thanks so much |
this is a VERY big problem with "university code"
it is often made by students that are NOT software developers and software engineers Geology writing code for geology programs Math majors writing code for a function Physics students writing astronomy software with help from the Geology students and so on some is good , some is GREAT, and some is a very messy bit of "spaghetti code" the "directions" are often a bit wrong or relate to 20+ year old instructions ( even if the software is new ) -- i build and use a lot of this stuff and " reading the code" is often better than trying to fallow the included instructions to have the OLD version of netcdf build " netcdf-4.2.1" is a OLD VERSION ! netcdf-4.3 is the current there is NO NEED to put libz.so in the netcdf-4.2.1 folder no need at all , you do NOT need to do that ! "./configure" will auto find it on the fedora 16 system using "autotools" that is WHY you run "configure" to set up a build script FOR YOUR SYSTEM setting "CPPFLAGS" and "LDFLAGS" in the terminal are not needed for almost ALL normal builds "configure" should auto take care of this yes way back in 1999 to 2003 they were NEEDED , but not today in 2013 -- sometimes for some "special" builds they are , but not 99.99999% of the time -- "university code" documentation -- sometimes it is VERY VERY OLD ,some of it dating from 1996 for netcdf Quote:
yum is the package manager Code:
su - Quote:
it auto made a folder( called /netcdf-4.2.1 ) when you extracted the gziped tarball "netcdf-4.2.1.tar.gz" also you DO NOT 100% DO NOT install the software to the build folder almost all older code , and a lot of new also , will AUTO configure to install to "/usr/local" fedora DOSE NOT , repeat dose NOT use that Debian default location it uses " /usr " by default you need to set that using "--prefix" in the configure line have a look at the default settings for netcdf-4.2.1 in that folder run this Code:
./configure --help Quote:
it is AUTO tested for and auto set to "yes" if needed Quote:
and the version of gcc that this program was DESIGNED for it is very likely that even on the now unsupported and old Fedora 16 that the version of gcc might be WAY too new -- just tested it on a fairly current gcc 4.7 , and it builds without an error PS. I just ONLY ran this and it build without any problems Code:
./configure -- for faster build times on a i5 or i7 or better CPU if you want to install it to "/home/usr/NETCDF well REPLACE "usr" with your REAL name -- the name on your home folder Code:
./configure --prefix=/home/fereshteh/NETCDF Code:
you will likely need to add that in the .bash_profile text file ( it is a hidden system file in your home folder run "make check" before you use it to check if there are problems or not all the tests should pass |
Moved: This thread is more suitable in Linux - General and has been moved accordingly to help your thread/question get the exposure it deserves.
Please use code-tags for output of commands and scripts. |
zlib
dear
thanks for your attention. i decide to use yum install zlib-devel (base on your recommendation) now how can i find its path to put in ./configure --with-zlib= ???? -prefix=/ / / netcdf for installing HDF5 and also netcdf. thanke so mush ;) |
# 13 :
zlib will be found automatically by applications that require zlib files. The same is valid for other libraries installed with yum. Why are you trying to build hdf5 and netcdf ? ? This will do for 99% of all applications : # yum install hdf5-devel netcdf-devel *** Which application is it that require hdf5 and netcdf ? ? - |
hdf5 and netcdf
actually ROMS model need hdf5 and netcdf libraries to determined in .bashrc file and roms bouild file too.
for this model it is need that i install netcdf with hdf5 and zlib too. and becouse i am newbie with roms and linux i try to install cmpeletly coincide with usergiude. in netcdf4 INSTALL guide write that i should install it with zlib and hdf5 by [code] Cd /home/fkomijani/zlib 1.2.7 ./configure --prefix=/home/fkomijani/NETCD4.2.1.1 make check install cd /home/fkomijani/HDF5 1.8.9 ./configure --with-zlib=/home/fkomijani/NETCD4.2.1.1 --prefix=//home/fkomijani/NETCD4.2.1.1 make check install and then cd /home/fkomijani/netcdf4.2.1.1 CPPFLAGS=-I/home/fkomijani/NETCD4.2.1.1/ include LDFLAGS=L/home/fkomijani/NETCD4.2.1.1 /lib ./configure --prefix=/home/fkomijani/NETCD4.2.1.1 make check install [code] i try to use it step by step (with out applying yum for installation) and now i install zlib by [code] yum install zlib-devel and i need guide for puting zlib path in --withzlib=.... part |
Are you trying to build a "static" version ?
if so then you will need to build zlib.a and use all NON dynamically linked libs |
dear my problem have not been sollved. i used
[code] yum install zlib yum install zlib-devel then with regard your answer that configure find zlib for installing hdf5 i use [code] [fereshteh@localhost ~]$ cd /home/fereshteh/hdf5-1.8.9 [fereshteh@localhost hdf5-1.8.9]$ ./configure --prefix=/home/fereshteh/HDF5 ./configure: line 2818: config.log: Permission denied ./configure: line 2828: config.log: Permission denied but as you can see those errors arised. what can i do now? thanks |
dont solved
dear my problem have not been sollved. i used
[code] yum install zlib yum install zlib-devel then with regard your answer that configure find zlib for installing hdf5 i use [code] [fereshteh@localhost ~]$ cd /home/fereshteh/hdf5-1.8.9 [fereshteh@localhost hdf5-1.8.9]$ ./configure --prefix=/home/fereshteh/HDF5 ./configure: line 2818: config.log: Permission denied ./configure: line 2828: config.log: Permission denied but as you can see those errors arised. what can i do now? also i like to say that i should not install hdf5 and netcdf with yum because my model (roms) need some setting that i should set their include and bin directories in different places. please help me without using yum thanks |
Quote:
autotools will auto find it it is is installed ( and it is already installed ) Quote:
that is not a good idea , it causes all kinds of problems delete the folder ( you might need to be root to do it ) then re extract the tar ball Also you have not answerer WHY you are trying to build from source a OLD VERSION 1.8.9 was released in May of 2012 the current 1.8.11 was released thin may (2013-05-08) and not the current version also WHY are you truing to build it ??? it should be in the fedora repos Code:
su - Quote:
" --prefix=/home/fereshteh/HDF5 " you MUST set the "bin" folder to "/home/fereshteh/HDF5/bin" and the include folder to "/home/fereshteh/HDF5/include" that is very "odd" the software default is the Debian "/usr/local " and fedora uses "/usr" instead so just where must you ? place? these bin and include folders fedora's default is /usr/bin /usr/include |
cc1
finally i use yum for installating zlib, hdf5 and netcdf, their versions are 1.2.6, 1.8.7 and 4.1.3 respectively. i know That netcdf include directory have to contains netcdf.mod, typesizes.mod , ncvalues.h, netcdf,h etc. But with yum installation first two files are set in /usr/lib/gfortran/modules path not in /usr/include, why ?in roms model i have to set NETCDF_INDIR that should set to one place for example /usr/include but as you can see 2 files are in /usr/lib/gfortran/modules? for this what is your recommendation. can i copy/paste those file to /usr/include?
Also when i compile roms with ./build.bash command this error arise [code] rm -f -r core *.ipo /home/fereshteh/projects/upwelling9/Build /home/fereshteh/make_macros.mk cpp: error trying to exec 'cc1': execvp: No such file or directory [code] i know that is about gcc compiler . When i type [code] [fereshteh@localhost upwelling9]$ whereis cc1 cc1: nothing replied. Would you please tell me how i can fix this error. Cheers fereshte |
usr/lib/gfortran/modules
is the correct install location the current autotools will find the modules if needed ldconf and pkgconfig will find them the instructions you might be fallowing are likely for the OLD folder and file system layout from 8 to 10 years ago for the older gcc tools . /usr/include is for the header files ( *.h ) these are in the devel rpms you really do not want to "copy / past" the usr/lib/gfortran/modules into /usr/include edit the makefile's in the project and NOT the operating system make_macros.mk m4 macros , a PHD theses can be done in trying to explain these but the upshot is the current macros used in the gcc 4 version is WAY better than the old versions in the old gcc3 tools "build.bash" edit the build files makefile projects REQUIRE you to manually edit the build files for your system |
cc1
thanks so mush for your answer.
for resolving my previous error (cpp: error trying to exec 'cc1': execvp: No such file or directory), i think that i should install another version of gcc (are you agree with me?).my current gcc version is 4.6.2 20111027(red hat 4.6.2-1)that have installed in my system by yum install gcc now would you please tell me how i can insall new version on fedora 16? and after installing i should changed default system setup to use new version of gcc? thanks in advance |
with out seeing the makefile for this makefile project
Quote:
-- i am assumming it is some project related to netcdf a search on that site shows this http://www.unidata.ucar.edu/googlere...df%2Findex.jsp cc1 is likely a alias for "makefile" projects you have to edit the makefile for YOUR system the autotools are not used this "make_macros.mk" is likely a hand wrote file how exactly did you install the whole gcc tool chain the way recommended by fedora has been to install the group Code:
su - fedora dose not really support that , there is the old gcc34 -compat a compatibility version but for say gcc 4.1 you must build that tool chain from source and take extreme care NOT to replace the currently installed gcc is designed to be installed "side by side" with other versions but take a month ( 30 days) and read up and study the subject first you might want to talk to your Prof. in this class about building this software or fallow the "contact us " link http://www.unidata.ucar.edu/about/index.html#contact the documentation i can find is for the CURRENT netcdf 4.3 http://www.unidata.ucar.edu/software.../building.html and is NOT for the old 4.2 you are using -- it might not apply to the old 4.2 version |
All times are GMT -5. The time now is 01:35 AM. |