topic Re: ifort command not found fedora8 in Intel® Fortran Compiler

ifort command not found fedora8

eren07 — Thu, 15 May 2008 12:58:01 GMT

Hi folks,
i have a fedora 8 installed computer, 64 bit with amd processor. but i have to use intel fortran compiler. i installed ifc 10.1.015 without any problem after i installed all the 'Development Tols'. then i configured the etc/profile file adding the last two lines:

# /etc/profile

# System wide environment and startup programs, for login setup
# Functions and aliases go in /etc/bashrc

pathmunge () {
if ! echo $PATH | /bin/egrep -q "(^|:)$1($|:)" ; then
if [ "$2" = "after" ] ; then
PATH=$PATH:$1
else
PATH=$1:$PATH
fi
fi
}

# ksh workaround
if [ -z "$EUID" -a -x /usr/bin/id ]; then
EUID=`id -u`
UID=`id -ru`
fi

# Path manipulation
if [ "$EUID" = "0" ]; then
pathmunge /sbin
pathmunge /usr/sbin
pathmunge /usr/local/sbin
fi

# No core files by default
ulimit -S -c 0 > /dev/null 2>&1

if [ -x /usr/bin/id ]; then
USER="`id -un`"
LOGNAME=$USER
MAIL="/var/spool/mail/$USER"
fi

HOSTNAME=`/bin/hostname`
HISTSIZE=1000

if [ -z "$INPUTRC" -a ! -f "$HOME/.inputrc" ]; then
INPUTRC=/etc/inputrc
fi

export PATH USER LOGNAME MAIL HOSTNAME HISTSIZE INPUTRC

for i in /etc/profile.d/*.sh ; do
if [ -r "$i" ]; then
. $i
fi
done

unset i
unset pathmunge
PATH=$PATH:/utilities:/opt/intel/fc/10.1.015/bin
export PATH

finally when i try to compile the program, i get the following warnings:

[root@Halserv utilities]# make
Making the sequential version
make[1]: Entering directory `/utilities'
make[2]: Entering directory `/utilities'
ifort -c -O -r8 -std95 -o parameters.o parameters.f90
make[2]: ifort: Command not found
make[2]: *** [libgibbs.a(parameters.o)] Error 127
make[2]: Leaving directory `/utilities'
make[1]: *** [libexe] Error 2
make[1]: Leaving directory `/utilities'
make: *** [sequential] Error 2

Is there anyone that can help me?
Thank you.

Re: ifort command not found fedora8

Steven_L_Intel1 — Thu, 15 May 2008 14:55:54 GMT

The 64-bit compiler is installed into /opt/intel/fce

I would also recommend using the "source" with the supplied ifortvars.sh as there's more than just PATH.

Re: ifort command not found fedora8

eren07 — Tue, 20 May 2008 11:19:29 GMT

Thank you Steve,
however, it was installed in fc directory as i checked it out.
and using source with or without path, did not work.

source /opt/intel/fc/10.1.015/bin/ifortvars.sh

Re: ifort command not found fedora8

Kevin_D_Intel — Tue, 20 May 2008 12:52:58 GMT

Steve suggested the subdirectory 'fce' in relation to your original post and the comment about the "64 bit with amd processor". If you are also running the 64-bit version of Fedora, then our installation would install the Intel 64 compiler under 'fce' sub-directory and not the 32-bit compiler which is found under 'fc'.

When you said using 'source' did not work. Does that mean you tried adding the source command in /etc/profile?

If so, after editing this file, did you log out and log back in, or start a new shell or, source /etc/profile to ensure your changes became active in your working shell?

Are you intended to run your makefile while logged in as root? Just asking since that is what you showed in your original post.

To provide us with some additional information, can you please execute the following commands and post the output in the issue:

/opt/intel/fc/10.1.015/bin/ifort -V
env

Re: ifort command not found fedora8

eren07 — Fri, 23 May 2008 14:52:44 GMT

Thank you for contributing the solution of the problem.
I used PATH=$PATH:/utilities:/opt/intel/fc/10.1.015/bin
command in terminal, then the ifort command worked, so my fortran program was installed without any problem (although source command in terminal with some problem), and finally it worked in the same terminal session.
however, i have to always use the path command to run my fortran program, and it is very difficult to do it for each windows.
i tried them in profile file (path command with; export PATH), but it was unsuccessful.
as you asked for

/opt/intel/fc/10.1.015/bin/ifort -V
env

commands, here are the resulting lines. Could you help about session problem?

[root@Halserv /]# /opt/intel/fc/10.1.015/bin/ifort -V
Intel Fortran Compiler for applications running on IA-32, Version 10.1 Build 20080312 Package ID: l_fc_p_10.1.015
Copyright (C) 1985-2008 Intel Corporation. All rights reserved.
FOR NON-COMMERCIAL USE ONLY

[root@Halserv /]# env
SSH_AGENT_PID=3095
SHELL=/bin/bash
DESKTOP_STARTUP_ID=
TERM=xterm
XDG_SESSION_COOKIE=e88b196d29d168ab7ca96e004820f700-1211549929.788528-977304023
GTK_RC_FILES=/etc/gtk/gtkrc:/root/.gtkrc-1.2-gnome2
WINDOWID=48234587
GTK_MODULES=gnomebreakpad
USER=root
LS_COLORS=no=00:fi=00:di=00;34:ln=00;36:pi=40;33:so=00;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=00;32:*.cmd=00;32:*.exe=00;32:*.com=00;32:*.btm=00;32:*.bat=00;32:*.sh=00;32:*.csh=00;32:*.tar=00;31:*.tgz=00;31:*.arj=00;31:*.taz=00;31:*.lzh=00;31:*.zip=00;31:*.z=00;31:*.Z=00;31:*.gz=00;31:*.bz2=00;31:*.bz=00;31:*.tz=00;31:*.rpm=00;31:*.cpio=00;31:*.jpg=00;35:*.gif=00;35:*.bmp=00;35:*.xbm=00;35:*.xpm=00;35:*.png=00;35:*.tif=00;35:
CCACHE_DIR=/var/cache/ccache
SSH_AUTH_SOCK=/tmp/ssh-FYMXWi3066/agent.3066
GNOME_KEYRING_SOCKET=/tmp/keyring-algh74/socket
SESSION_MANAGER=local/unix:@/tmp/.ICE-unix/3066,unix/unix:/tmp/.ICE-unix/3066
DESKTOP_SESSION=default
PATH=/usr/kerberos/sbin:/usr/kerberos/bin:/usr/lib/ccache:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin
GDM_XSERVER_LOCATION=local
PWD=/
CCACHE_UMASK=002
KDE_IS_PRELINKED=1
LANG=C
GNOME_KEYRING_PID=3064
GDM_LANG=C
KDEDIRS=/usr
GDMSESSION=default
SSH_ASKPASS=/usr/libexec/openssh/gnome-ssh-askpass
HOME=/root
SHLVL=2
GNOME_DESKTOP_SESSION_ID=Default
LOGNAME=root
CVS_RSH=ssh
XDG_DATA_DIRS=/usr/local/share/:/usr/share/:/usr/share/gdm/
DBUS_SESSION_BUS_ADDRESS=unix:abstract=/tmp/dbus-4BENFWm4hs,guid=c3ec21ea3390c5e3fb4c82004836c8e9
LESSOPEN=|/usr/bin/lesspipe.sh %s
WINDOWPATH=7:7
DISPLAY=:0.0
G_BROKEN_FILENAMES=1
COLORTERM=gnome-terminal
XAUTHORITY=/tmp/.gdmO02UBU
OLDPWD=/root
_=/bin/env

Re: ifort command not found fedora8

Kevin_D_Intel — Fri, 23 May 2008 16:21:10 GMT

Your last post shows you have the IA-32 compiler installed, which suggest you probably are also running the 32-bit version of Fedora Core 8. Since you opened this thread indicating your system contains a 64-bit AMD processor, if thats true, then you wont realize the full potential of your cpu with the choice of OS and compiler. For that you need to use the 64-bit (x86_64) version of Fedora Core 8, and then the Intel compiler installer will install the Intel 64 compiler, not the IA-32 compiler.

It is nearly impossible to assist with your issues involving /etc/profile and the source command in the absence of seeing a context of what you state is not working. If you can provide details for errors you received or what is meant by it was unsuccessful then we can try to help.

Your env output shows a couple of things:

You are still using the root account. Maybe thats what you intend, but thats not typical
Theres no evidence the PATH setting was set as you described, meaning theres no path to ifort

If you suffer an error when using the command: source /opt/intel/fc/10.1.015/bin/ifortvars.sh then please tell us what that error is.

After editing /etc/profile what do you mean when you say it was unsuccessful?

What was unsuccessful?

After editing /etc/profile it is imperative that you do one of the following actions so the changes take effect:

Completely logoff your system and log back in and restart any Xterm or terminal windows, then check the PATH setting or execute: ifort -V
Enter the command: source /etc/profile in the current window, then check the PATH setting or execute: ifort -V
Spawn a new shell from the current window so that /etc/profile is read, then check the PATH setting or execute: ifort -V

The preferred action is option 1 above. The point of changing /etc/profile is to ensure that when users log into your system their environment is setup as you desire with a path to ifort.

If you are not trying to make a system-wide change for all users, then assuming your personal account default login shell is BASH, a better alternative to editing /etc/profile is to edit your personal user accounts $HOME/.bash_profile or $HOME/.bash_rc to add the command to source the ifortvars.sh setup script.

I know you keep focusing on only setting the PATH variable to the bin sub-directory to run ifort, but believe us when we tell you this is not sufficient. If you get your program compiled and produce an executable it is likely the execution will fail due to you not having LD_LIBRARY_PATH set accordingly to load necessary ifort related shared libraries.

To resolve what you are trying to accomplish, you should focus on entering the source command mentioned earlier in /etc/profile or either your personal $HOME/.bash_profile or $HOME/.bash_rc files as mentioned.

Re: ifort command not found fedora8

eren07 — Tue, 27 May 2008 12:16:00 GMT

As you said, it must be 32bit-fc. First of all, i tried your suggestions after adding the source line into etc/profile file and logging off and then back in. Here is the output:
[root@Halserv /]# ifort -V
bash: ifort: command not found
[root@Halserv /]# source /etc/profile
: command not found
: command not found
'ash: /etc/profile: line 6: syntax error near unexpected token `{
'ash: /etc/profile: line 6: `pathmunge () {
[root@Halserv /]# ifort -V
bash: ifort: command not found

This is my profile file:
# /etc/profile

# System wide environment and startup programs, for login setup
# Functions and aliases go in /etc/bashrc

pathmunge () {
if ! echo $PATH | /bin/egrep -q "(^|:)$1($|:)" ; then
if [ "$2" = "after" ] ; then
PATH=$PATH:$1
else
PATH=$1:$PATH
fi
fi
}

# ksh workaround
if [ -z "$EUID" -a -x /usr/bin/id ]; then
EUID=`id -u`
UID=`id -ru`
fi

# Path manipulation
if [ "$EUID" = "0" ]; then
pathmunge /sbin
pathmunge /usr/sbin
pathmunge /usr/local/sbin
fi

# No core files by default
ulimit -S -c 0 > /dev/null 2>&1

if [ -x /usr/bin/id ]; then
USER="`id -un`"
LOGNAME=$USER
MAIL="/var/spool/mail/$USER"
fi

HOSTNAME=`/bin/hostname`
HISTSIZE=1000

if [ -z "$INPUTRC" -a ! -f "$HOME/.inputrc" ]; then
INPUTRC=/etc/inputrc
fi

export PATH USER LOGNAME MAIL HOSTNAME HISTSIZE INPUTRC

for i in /etc/profile.d/*.sh ; do
if [ -r "$i" ]; then
. $i
fi
done

unset i
unset pathmunge
source /opt/intel/fce/10.1.015/bin/ifortvars.sh

I have the same file (except the last line, it has the "PATH" line) in another fc5 installed pc, however it has no problem.

I meant saying unsuccessful that executable file command had not been found. Therefore, i tried the same procedure to write the output. I installed the gibbs package program with make command, however when i use gibbs.exe command without path command, it fails. I have to always write the path command in each window.
This is the output, when i used the source command in terminal:

[root@Halserv utilities]# make
Making the sequential version
make[1]: Entering directory `/utilities'
perl ./makeDepends.pl ./Makefile.depends . gibbs gibbs.f90 generic.f90 parameters.f90 common.f90 timing.f90 random.f90 adjust_param.f90 aua_model.f90 energy.f90 pressure.f90 utilities.f90 electrostatic.f90 update_transfer.f90 induction.f90 volume_change.f90 gdeR.f90 rotate_mol.f90 translate_mol.f90 regrow_CBMC.f90 read_write.f90 initconf_mol.f90 cycle.f90 create_initconf.f90 relax_rigid.f90 int_config_mol.f90 transfer_mol.f90 int_ro t_ssb.f90 reptation.f90 conrot.f90 gcmc.f90 branched.f90 pivot.f90 displacement.f90 swap.f90 mod_main.f90 dble_bridging.f90 trimer.f90 int_dble_rebridging.f90 fakeMpi.f90
make[2]: Entering directory `/utilities'
ifort -c -O -r8 -std95 -o parameters.o parameters.f90
make[2]: ifort: Command not found
make[2]: *** [libgibbs.a(parameters.o)] Error 127
make[2]: Leaving directory `/utilities'
make[1]: *** [libexe] Error 2
make[1]: Leaving directory `/utilities'
make: *** [sequential] Error 2
[root@Halserv utilities]# source /opt/intel/fc/10.1.015/bin/ifortvars.sh
[root@Halserv utilities]# make
Making the sequential version
make[1]: Entering directory `/utilities'
make[2]: Entering directory `/utilities'
ifort -c -O -r8 -std95 -o parameters.o parameters.f90
/usr/bin/ar rv ./libgibbs.a parameters.o
/usr/bin/ar: creating ./libgibbs.a
a - parameters.o
/bin/rm -f parameters.o
ifort -c -O -r8 -std95 -o common.o common.f90
/usr/bin/ar rv ./libgibbs.a common.o
a - common.o
/bin/rm -f common.o
ifort -c -O -r8 -std95 -o adjust_param.o adjust_param.f90
/usr/bin/ar rv ./libgibbs.a adjust_param.o
a - adjust_param.o
/bin/rm -f adjust_param.o
ifort -c -O -r8 -std95 -o gdeR.o gdeR.f90
/usr/bin/ar rv ./libgibbs.a gdeR.o
a - gdeR.o
/bin/rm -f gdeR.o
ifort -c -O -r8 -std95 -o energy.o energy.f90
/usr/bin/ar rv ./libgibbs.a energy.o
a - energy.o
/bin/rm -f energy.o
ifort -c -O -r8 -std95 -o pressure.o pressure.f90
/usr/bin/ar rv ./libgibbs.a pressure.o
a - pressure.o
/bin/rm -f pressure.o
ifort -c -O -r8 -std95 -o random.o random.f90
/usr/bin/ar rv ./libgibbs.a random.o
a - random.o
/bin/rm -f random.o
ifort -c -O -r8 -std95 -o utilities.o utilities.f90
/usr/bin/ar rv ./libgibbs.a utilities.o
a - utilities.o
/bin/rm -f utilities.o
ifort -c -O -r8 -std95 -o initconf_mol.o initconf_mol.f90
/usr/bin/ar rv ./libgibbs.a initconf_mol.o
a - initconf_mol.o
/bin/rm -f initconf_mol.o
ifort -c -O -r8 -std95 -o fakeMpi.o fakeMpi.f90
/usr/bin/ar rv ./libgibbs.a fakeMpi.o
a - fakeMpi.o
/bin/rm -f fakeMpi.o
ifort -c -O -r8 -std95 -o induction.o induction.f90
/usr/bin/ar rv ./libgibbs.a induction.o
a - induction.o
/bin/rm -f induction.o
ifort -c -O -r8 -std95 -o aua_model.o aua_model.f90
/usr/bin/ar rv ./libgibbs.a aua_model.o
a - aua_model.o
/bin/rm -f aua_model.o
ifort -c -O -r8 -std95 -o regrow_CBMC.o regrow_CBMC.f90
/usr/bin/ar rv ./libgibbs.a regrow_CBMC.o
a - regrow_CBMC.o
/bin/rm -f regrow_CBMC.o
ifort -c -O -r8 -std95 -o cycle.o cycle.f90
/usr/bin/ar rv ./libgibbs.a cycle.o
a - cycle.o
/bin/rm -f cycle.o
ifort -c -O -r8 -std95 -o electrostatic.o electrostatic.f90
/usr/bin/ar rv ./libgibbs.a electrostatic.o
a - electrostatic.o
/bin/rm -f electrostatic.o
ifort -c -O -r8 -std95 -o relax_rigid.o relax_rigid.f90
/usr/bin/ar rv ./libgibbs.a relax_rigid.o
a - relax_rigid.o
/bin/rm -f relax_rigid.o
ifort -c -O -r8 -std95 -o update_transfer.o update_transfer.f90
/usr/bin/ar rv ./libgibbs.a update_transfer.o
a - update_transfer.o
/bin/rm -f update_transfer.o
ifort -c -O -r8 -std95 -o transfer_mol.o transfer_mol.f90
/usr/bin/ar rv ./libgibbs.a transfer_mol.o
a - transfer_mol.o
/bin/rm -f transfer_mol.o
ifort -c -O -r8 -std95 -o timing.o timing.f90
/usr/bin/ar rv ./libgibbs.a timing.o
a - timing.o
/bin/rm -f timing.o
ifort -c -O -r8 -std95 -o translate_mol.o translate_mol.f90
/usr/bin/ar rv ./libgibbs.a translate_mol.o
a - translate_mol.o
/bin/rm -f translate_mol.o
ifort -c -O -r8 -std95 -o trimer.o trimer.f90
/usr/bin/ar rv ./libgibbs.a trimer.o
a - trimer.o
/bin/rm -f trimer.o
ifort -c -O -r8 -std95 -o conrot.o conrot.f90
/usr/bin/ar rv ./libgibbs.a conrot.o
a - conrot.o
/bin/rm -f conrot.o
ifort -c -O -r8 -std95 -o dble_bridging.o dble_bridging.f90
/usr/bin/ar rv ./libgibbs.a dble_bridging.o
a - dble_bridging.o
/bin/rm -f dble_bridging.o
ifort -c -O -r8 -std95 -o swap.o swap.f90
/usr/bin/ar rv ./libgibbs.a swap.o
a - swap.o
/bin/rm -f swap.o
ifort -c -O -r8 -std95 -o displacement.o displacement.f90
/usr/bin/ar rv ./libgibbs.a displacement.o
a - displacement.o
/bin/rm -f displacement.o
ifort -c -O -r8 -std95 -o branched.o branched.f90
/usr/bin/ar rv ./libgibbs.a branched.o
a - branched.o
/bin/rm -f branched.o
ifort -c -O -r8 -std95 -o read_write.o read_write.f90
fortcom: Warning: read_write.f90, line 2287: Extension to standard: The text exceeds right hand column allowed on the line.
read (1,*) mix_rule ! 1 = Lorentz-Berthelot ; 2 = Kong ; 3 = Waldmann - Hagler ; 4 = geometric on sigma and epsilon -- default value in name list: 1
------------------------------------------------------------------------------------------------------------------------------------^
fortcom: Warning: read_write.f90, line 2315: Extension to standard: The text exceeds right hand column allowed on the line.
read (1,*) induction ! true if induction energy (i.e. polarisation) is considered ; false else -- default value in name list: false
------------------------------------------------------------------------------------------------------------------------------------^
fortcom: Warning: read_write.f90, line 2377: Extension to standard: The text exceeds right hand column allowed on the line.
read (1,*) setpoint ! target acceptance for rotations, translations, volume changes -- default value in name list: 0.5
------------------------------------------------------------------------------------------------------------------------------------^
fortcom: Warning: read_write.f90, line 2381: Extension to standard: The text exceeds right hand column allowed on the line.
read (1,*) cutoff2 ! cutoff radius, angstroem (if zero, cutoff is set to smallest half box length) -- default value in name list: 0.
------------------------------------------------------------------------------------------------------------------------------------^
fortcom: Warning: read_write.f90, line 7539: Parentheses around an I/O list is an extension to Standard F95. [MU]
(Mu(i,1))
-----------^
/usr/bin/ar rv ./libgibbs.a read_write.o
a - read_write.o
/bin/rm -f read_write.o
ifort -c -O -r8 -std95 -o int_config_mol.o int_config_mol.f90
/usr/bin/ar rv ./libgibbs.a int_config_mol.o
a - int_config_mol.o
/bin/rm -f int_config_mol.o
ifort -c -O -r8 -std95 -o pivot.o pivot.f90
/usr/bin/ar rv ./libgibbs.a pivot.o
a - pivot.o
/bin/rm -f pivot.o
ifort -c -O -r8 -std95 -o reptation.o reptation.f90
/usr/bin/ar rv ./libgibbs.a reptation.o
a - reptation.o
/bin/rm -f reptation.o
ifort -c -O -r8 -std95 -o gcmc.o gcmc.f90
/usr/bin/ar rv ./libgibbs.a gcmc.o
a - gcmc.o
/bin/rm -f gcmc.o
ifort -c -O -r8 -std95 -o rotate_mol.o rotate_mol.f90
/usr/bin/ar rv ./libgibbs.a rotate_mol.o
a - rotate_mol.o
/bin/rm -f rotate_mol.o
ifort -c -O -r8 -std95 -o volume_change.o volume_change.f90
/usr/bin/ar rv ./libgibbs.a volume_change.o
a - volume_change.o
/bin/rm -f volume_change.o
ifort -c -O -r8 -std95 -o create_initconf.o create_initconf.f90
/usr/bin/ar rv ./libgibbs.a create_initconf.o
a - create_initconf.o
/bin/rm -f create_initconf.o
ifort -c -O -r8 -std95 -o int_dble_rebridging.o int_dble_rebridging.f90
/usr/bin/ar rv ./libgibbs.a int_dble_rebridging.o
a - int_dble_rebridging.o
/bin/rm -f int_dble_rebridging.o
ifort -c -O -r8 -std95 -o int_rot_ssb.o int_rot_ssb.f90
/usr/bin/ar rv ./libgibbs.a int_rot_ssb.o
a - int_rot_ssb.o
/bin/rm -f int_rot_ssb.o
ifort -c -O -r8 -std95 -o mod_main.o mod_main.f90
/usr/bin/ar rv ./libgibbs.a mod_main.o
a - mod_main.o
/bin/rm -f mod_main.o
ifort -c -O -r8 -std95 -o gibbs.o gibbs.f90
ifort -c -O -r8 -std95 -o generic.o generic.f90
/usr/bin/ar rv ./libgibbs.a generic.o
a - generic.o
/bin/rm -f generic.o
ifort -o gibbs.exe gibbs.o -L. -lgibbs -static-libcxa
ifort: command line remark #10010: option '-static-libcxa' is deprecated and will be removed in a future release. See '-help deprecated'
make[2]: Leaving directory `/utilities'
make[1]: Leaving directory `/utilities'
[root@Halserv utilities]# gibbs.exe
bash: gibbs.exe: command not found

This is the output, when i used the path command in terminal (gibbs command worked but needed data files):

[root@Halserv utilities]# make
Making the sequential version
make[1]: Entering directory `/utilities'
perl ./makeDepends.pl ./Makefile.depends . gibbs gibbs.f90 generic.f90 parameters.f90 common.f90 timing.f90 random.f90 adjust_param.f90 aua_model.f90 energy.f90 pressure.f90 utilities.f90 electrostatic.f90 update_transfer.f90 induction.f90 volume_change.f90 gdeR.f90 rotate_mol.f90 translate_mol.f90 regrow_CBMC.f90 read_write.f90 initconf_mol.f90 cycle.f90 create_initconf.f90 relax_rigid.f90 int_config_mol.f90 transfer_mol.f90 int_rot_ssb.f90 reptation.f90 conrot.f90 gcmc.f90 branched.f90 pivot.f90 displacement.f90 swap.f90 mod_main.f90 dble_bridging.f90 trimer.f90 int_dble_rebridging.f90 fakeMpi.f90
make[2]: Entering directory `/utilities'
ifort -c -O -r8 -std95 -o parameters.o parameters.f90
make[2]: ifort: Command not found
make[2]: *** [libgibbs.a(parameters.o)] Error 127
make[2]: Leaving directory `/utilities'
make[1]: *** [libexe] Error 2
make[1]: Leaving directory `/utilities'
make: *** [sequential] Error 2
[root@Halserv utilities]# PATH=$PATH:/utilities:/opt/intel/fc/10.1.015/bin
[root@Halserv utilities]# make
Making the sequential version
make[1]: Entering directory `/utilities'
make[2]: Entering directory `/utilities'
ifort -c -O -r8 -std95 -o parameters.o parameters.f90
/usr/bin/ar rv ./libgibbs.a parameters.o
/usr/bin/ar: creating ./libg ibbs.a
a - parameters.o
/bin/rm -f parameters.o
ifort -c -O -r8 -std95 -o common.o common.f90
/usr/bin/ar rv ./libgibbs.a common.o
a - common.o
/bin/rm -f common.o
ifort -c -O -r8 -std95 -o adjust_param.o adjust_param.f90
/usr/bin/ar rv ./libgibbs.a adjust_param.o
a - adjust_param.o
/bin/rm -f adjust_param.o
ifort -c -O -r8 -std95 -o gdeR.o gdeR.f90
/usr/bin/ar rv ./libgibbs.a gdeR.o
a - gdeR.o
/bin/rm -f gdeR.o
ifort -c -O -r8 -std95 -o energy.o energy.f90
/usr/bin/ar rv ./libgibbs.a energy.o
a - energy.o
/bin/rm -f energy.o
ifort -c -O -r8 -std95 -o pressure.o pressure.f90
/usr/bin/ar rv ./libgibbs.a pressure.o
a - pressure.o
/bin/rm -f pressure.o
ifort -c -O -r8 -std95 -o random.o random.f90
/usr/bin/ar rv ./libgibbs.a random.o
a - random.o
/bin/rm -f random.o
ifort -c -O -r8 -std95 -o utilities.o utilities.f90
/usr/bin/ar rv ./libgibbs.a utilities.o
a - utilities.o
/bin/rm -f utilities.o
ifort -c -O -r8 -std95 -o initconf_mol.o initconf_mol.f90
/usr/bin/ar rv ./libgibbs.a initconf_mol.o
a - initconf_mol.o
/bin/rm -f initconf_mol.o
ifort -c -O -r8 -std95 -o fakeMpi.o fakeMpi.f90
/usr/bin/ar rv ./libgibbs.a fakeMpi.o
a - fakeMpi.o
/bin/rm -f fakeMpi.o
ifort -c -O -r8 -std95 -o induction.o induction.f90
/usr/bin/ar rv ./libgibbs.a induction.o
a - induction.o
/bin/rm -f induction.o
ifort -c -O -r8 -std95 -o aua_model.o aua_model.f90
/usr/bin/ar rv ./libgibbs.a aua_model.o
a - aua_model.o
/bin/rm -f aua_model.o
ifort -c -O -r8 -std95 -o regrow_CBMC.o regrow_CBMC.f90
/usr/bin/ar rv ./libgibbs.a regrow_CBMC.o
a - regrow_CBMC.o
/bin/rm -f regrow_CBMC.o
ifort -c -O -r8 -std95 -o cycle.o cycle.f90
/usr/bin/ar rv ./libgibbs.a cycle.o
a - cycle.o
/bin/rm -f cycle.o
ifort -c -O -r8 -std95 -o electrostatic.o electrostatic.f90
/usr/bin/ar rv ./libgibbs.a electrostatic.o
a - electrostatic.o
/bin/rm -f electrostatic.o
ifort -c -O -r8 -std95 -o relax_rigid.o relax_rigid.f90
/usr/bin/ar rv ./libgibbs.a relax_rigid.o
a - relax_rigid.o
/bin/rm -f relax_rigid.o
ifort -c -O -r8 -std95 -o update_transfer.o update_transfer.f90
/usr/bin/ar rv ./libgibbs.a update_transfer.o
a - update_transfer.o
/bin/rm -f update_transfer.o
ifort -c -O -r8 -std95 -o transfer_mol.o transfer_mol.f90
/usr/bin/ar rv ./libgibbs.a transfer_mol.o
a - transfer_mol.o
/bin/rm -f transfer_mol.o
ifort -c -O -r8 -std95 -o timing.o timing.f90
/usr/bin/ar rv ./libgibbs.a timing.o
a - timing.o
/bin/rm -f timing.o
ifort -c -O -r8 -std95 -o translate_mol.o translate_mol.f90
/usr/bin/ar rv ./libgibbs.a translate_mol.o
a - translate_mol.o
/bin/rm -f translate_mol.o
ifort -c -O -r8 -std95 -o trimer.o trimer.f90
/usr/bin/ar rv ./libgibbs.a trimer.o
a - trimer.o
/bin/rm -f trimer.o
ifort -c -O -r8 -std95 -o conrot.o conrot.f90
/usr/bin/ar rv ./libgibbs.a conrot.o
a - conrot.o
/bin/rm -f conrot.o
ifort -c -O -r8 -std95 -o dble_bridging.o dble_bridging.f90
/usr/bin/ar rv ./libgibbs.a dble_bridging.o
a - dble_bridging.o
/bin/rm -f dble_bridging.o
ifort -c -O -r8 -std95 -o swap.o swap.f90
/usr/bin/ar rv ./libgibbs.a swap.o
a - swap.o
/bin/rm -f swap.o
ifort -c -O -r8 -std95 -o displacement.o displacement.f90
/usr/bin/ar rv ./libgibbs.a displacement.o
a - displacement.o
/bin/rm -f displacement.o
ifort -c -O -r8 -std95 -o branched.o branched.f90
/usr/bin/ar rv ./libgibbs.a branched.o
a - branched.o
/bin/rm -f branched.o
ifort -c -O -r8 -std95 -o read_write.o read_write.f90
fortcom: Warning: read_write.f90, line 2287: Extension to standard: The text exceeds right hand column allowed on the line.
read (1,*) mix_rule ! 1 = Lorentz-Berthelot ; 2 = Kong ; 3 = Waldmann - Hagler ; 4 = geometric on sigma and epsilon -- default value in name list: 1
------------------------------------------------------------------------------------------------------------------------------------^
fortcom: Warning: read_write.f90, line 2315: Extension to standard: The text exceeds right hand column allowed on the line.
read (1,*) induction ! true if induction energy (i.e. polarisation) is considered ; false else -- default value in name list: false
------------------------------------------------------------------------------------------------------------------------------------^
fortcom: Warning: read_write.f90, line 2377: Extension to standard: The text exceeds right hand column allowed on the line.
read (1,*) setpoint ! target acceptance for rotations, translations, volume changes -- default value in name list: 0.5
------------------------------------------------------------------------------------------------------------------------------------^
fortcom: Warning: read_write.f90, line 2381: Extension to standard: The text exceeds right hand column allowed on the line.
read (1,*) cutoff2 ! cutoff radius, angstroem (if zero, cutoff is set to smallest half box length) -- default value in name list: 0.
------------------------------------------------------------------------------------------------------------------------------------^
fortcom: Warning: read_write.f90, line 7539: Parentheses around an I/O list is an extension to Standard F95. [MU]
(Mu(i,1))
-----------^
/usr/bin/ar rv ./libgibbs.a read_write.o
a - read_write.o
/bin/rm -f read_write.o
ifort -c -O -r8 -std95 -o int_config_mol.o int_config_mol.f90
/usr/bin/ar rv ./libgibbs.a int_config_mol.o
a - int_config_mol.o
/bin/rm -f int_config_mol.o
ifort -c -O -r8 -std95 -o pivot.o pivot.f90
/usr/bin/ar rv ./libgibbs.a pivot.o
a - pivot.o
/bin/rm -f pivot.o
ifort -c -O -r8 -std95 -o reptation.o reptation.f90
/usr/bin/ar rv ./libgibbs.a reptation.o
a - reptation.o
/bin/rm -f reptation.o
ifort -c -O -r8 -std95 -o gcmc.o gcmc.f90
/usr/bin/ar rv ./libgibbs.a gcmc.o
a - gcmc.o
/bin/rm -f gcmc.o
ifort -c -O -r8 -std95 -o rotate_mol.o rotate_mol.f90
/usr/bin/ar rv ./libgibbs.a rotate_mol.o
a - rotate_mol.o
/bin/rm -f rotate_mol.o
ifort -c -O -r8 -std95 -o volume_change.o volume_change.f90
/usr/bin/ar rv ./libgibbs.a volume_change.o
a - volume_change.o
/bin/rm -f volume_change.o
ifort -c -O -r8 -std95 -o create_initconf.o create_initconf.f90
/usr/bin/ar rv ./libgibbs.a create_initconf.o
a - create_initconf.o
/bin/rm -f create_initconf.o
ifort -c -O -r8 -std95 -o int_dble_rebridging.o int_dble_rebridging.f90
/usr/bin/ar rv ./libgibbs.a int_dble_rebridging.o
a - int_dble_rebridging.o
/bin/rm -f int_dble_rebridging.o
ifort -c -O -r8 -std95 -o int_rot_ssb.o int_rot_ssb.f90
/usr/bin/ar rv ./libgibbs.a int_rot_ssb.o
a - int_rot_ssb.o
/bin/rm -f int_rot_ssb.o
ifort -c -O -r8 -std95 -o mod_main.o mod_main.f90
/usr/bin/ar rv ./libgibbs.a mod_main.o
a - mod_main.o
/bin/rm -f mod_main.o
ifort -c -O -r8 -std95 -o gibbs.o gibbs.f90
ifort -c -O -r8 -std95 -o generic.o generic.f90
/usr/bin/ar rv ./libgibbs.a generic.o
a - generic.o
/bin/rm -f generic.o
ifort -o gibbs.exe gibbs.o -L. -lgibbs -static-libcxa
ifort: command line remark #10010: option '-static-libcxa' is deprecated and will be removed in a future release. See '-help deprecated'
make[2]: Leaving directory `/utilities'
make[1]: Leaving directory `/utilities'
[root@Halserv utilities]# gibbs.exe
The output file is redirected to gibbs.log
forrtl: severe (24): end-of-file during read, unit 1, file /utilities/potparam.dat
Image PC Routine Line Source
gibbs.exe 0827095B Unknown Unknown Unknown
gibbs.exe 0826FF7B Unknown Unknown Unknown
gibbs.exe 0823352E Unknown Unknown Unknown
gibbs.exe 081F2D52 Unknown Unknown Unknown
gibbs.exe 081F29ED Unknown Unknown Unknown
gibbs.exe 0820DFAB Unknown Unknown Unknown
gibbs.exe 08148A51 Unknown Unknown Unknown
gibbs.exe 08151798 Unknown Unknown Unknown
gibbs.exe 0804A213 Unknown Unknown Unknown
gibbs.exe 08049F01 Unknown Unknown Unknown
libc.so.6 006DE390 Unknown Unknown Unknown
gibbs.exe 08049E11 Unknown&nb sp; Unknown Unknown

Could you tell me how to use it witout writing any command before gibbs.exe for all users?
Thank you (sorry for this long message)!

Re: ifort command not found fedora8

Kevin_D_Intel — Mon, 02 Jun 2008 23:23:37 GMT

If you have not noticed yet, the edit you made to the /etc/profile references the fce directory when sourcing ifortvars.sh but that directory does not exist on your system since you installed the IA-32 compiler. The reason it worked when you sourced ifortvars.sh interactively is because you referenced the fc subdirectory.

You should add the following line to /etc/profile:

source /opt/intel/fc/10.1.015/bin/ifortvars.sh

Note that the path above references the fc subdirectory. Once you make the correct edit to the /etc/profile your current system should work fine like your FC5 system.

Re: ifort command not found fedora8

eren07 — Fri, 06 Jun 2008 10:36:02 GMT

I corrected the last line of etc/profile as source /opt/intel/fc/10.1.015/bin/ifortvars.sh
and logged off and back in. Then I used the same coomads as in the green written message, however the same lines come back as in the green message.

Re: ifort command not found fedora8

Kevin_D_Intel — Fri, 06 Jun 2008 16:20:23 GMT

If you edit /etc/profile then logoff/login there is no need to source /etc/profile again.

The errors you received in green you earlier post for the ifort command not found and using the source command suggest that you have broken the /etc/profile file near line 6 while trying to edit the file. The file content you included in your earlier postshaded red I expect does not reflect what is actually on your system now. If you have backup of the file, then restore the file from the backup and edit the file again and only add the last line we have been discussing to source the ifortvars.sh script.

If you do not have a backup, then check to make sure that line 6 reads as follows:

pathmunge () {

Perhaps in editing you accidentally removed a paren or curly bracket. If you want to paste the current /etc/profile content into a reply then perhaps we can spot the issue.

Re: ifort command not found fedora8

eren07 — Mon, 09 Jun 2008 09:01:30 GMT

This is my original etc/profile file, which is the same as the file in the fc5 installed computer, except the last line:

# /etc/profile

# System wide environment and startup programs, for login setup
# Functions and aliases go in /etc/bashrc

pathmunge () {
if ! echo $PATH | /bin/egrep -q "(^|:)$1($|:)" ; then
if [ "$2" = "after" ] ; then
PATH=$PATH:$1
else
PATH=$1:$PATH
fi
fi
}

# ksh workaround
if [ -z "$EUID" -a -x /usr/bin/id ]; then
EUID=`id -u`
UID=`id -ru`
fi

# Path manipulation
if [ "$EUID" = "0" ]; then
pathmunge /sbin
pathmunge /usr/sbin
pathmunge /usr/local/sbin
fi

# No core files by default
ulimit -S -c 0 > /dev/null 2>&1

if [ -x /usr/bin/id ]; then
USER="`id -un`"
LOGNAME=$USER
MAIL="/var/spool/mail/$USER"
fi

HOSTNAME=`/bin/hostname`
HISTSIZE=1000

if [ -z "$INPUTRC" -a ! -f "$HOME/.inputrc" ]; then
INPUTRC=/etc/inputrc
fi

export PATH USER LOGNAME MAIL HOSTNAME HISTSIZE INPUTRC

for i in /etc/profile.d/*.sh ; do
if [ -r "$i" ]; then
. $i
fi
done

unset i
unset pathmunge
source /opt/intel/fc/10.1.015/bin/ifortvars.sh

then i make some changes in the file, here are the results:

[root@Halserv /]# source /etc/profile
: command not found
: command not found
'ash: /etc/profile: line 6: syntax error near unexpected token `{
'ash: /etc/profile: line 6: `pathmunge () {
[root@Halserv /]# source /etc/profile
: command not found
: command not found
'ash: /etc/profile: line 6: syntax error near unexpected token `
'ash: /etc/profile: line 6: `pathmunge ()
[root@Halserv /]# source /etc/profile
: command not found
: command not found
: command not found
'ash: /etc/profile: line 47: syntax error near unexpected token `do
'ash: /etc/profile: line 47: `for i in /etc/profile.d/*.sh ; do
[root@Halserv /]# source /etc/profile
: command not found
: command not found
: command not found
'ash: /etc/profile: line 47: syntax error near unexpected token `
'ash: /etc/profile: line 47: `for i in /etc/profile.d/*.sh ;
[root@Halserv /]# source /etc/profile
: command not found
: command not found
: command not found
bash: /etc/profile: line 55: syntax error: unexpected end of file

finally i tried some changes in the last line (source line), however the same error was on the screen.

Re: ifort command not found fedora8

Kevin_D_Intel — Mon, 09 Jun 2008 14:48:44 GMT

First, before trying the suggestions below, please log out and log back into your system.

Next, report what processes are listed when you execute the command: ps

Next, edit /etc/profile and add the following lines in the file where indicated:

1. Add the following line to become line 1 of the file:

set x

2. Add the following list to become the last line in the file (after the source of the ifortvars.sh):

set +x

Then run this command:

source /etc/profile &> /tmp/prof.out

Make sure this file contains some useful output and then attach the file /tmp/prof.out to this Forum thread. The file attach mechanism is located on the Options tab when you are composing a reply.

Perhaps the issue involves the initial PATH setting. Sourcing /etc/profile repeatedly is likely just garbling your PATH variable.

Re: ifort command not found fedora8

eren07 — Thu, 12 Jun 2008 10:28:14 GMT

I tried to add set line with the original form (prof1 file), then i tried with correcting the errors, except the last line with set line (prof2 ) file. Finally i have added the ps command result.

Re: ifort command not found fedora8

Kevin_D_Intel — Thu, 12 Jun 2008 18:22:08 GMT

Whatever editor you used to edit the file has seemingly converted it into UTF-8 Unicode text format which bash is unable to parse. I get the same errors as you on my system trying to use both copies of profile you provided.

Try downloading the attached copy I provided. Rename your existing copies to have a suffix of .sav or .old, and then rename the file I provided to be just profile and then retry the source command again.

You should not see any errors (hopefully) and you should then be able to execute: which ifort and see that ifort is found.

If that works, then you need to determine whats different between the editors on your FC8 and FC5 systems.

Re: ifort command not found fedora8

eren07 — Mon, 16 Jun 2008 09:50:16 GMT

First of all, thank you very much Mr. Davis for your help.
The problem is solved. I used your profile file copy, and i had the outputs in the attached file. However, the program did not work with source line, then i changed it with path line.After the change, it worked without any problem.
My text editor in fc5 computer is gedit 2.15.9, and the editor in fc8 is gedit 2.20.3.