Re: [ccp4bb] CNS installation
Hello Ben, Thanks a lot. After your mail, I looked up your suggestions in old thread on cnsbb. Installed gfortran and built as you suggested. It worked very well. Thanks Yogi > Date: Sat, 28 Jul 2012 17:18:09 -0400 > From: b...@hkl.hms.harvard.edu > Subject: Re: [ccp4bb] CNS installation > To: CCP4BB@JISCMAIL.AC.UK > > Hi Rajesh, > > > Hello Ed, I have is 32 bit pc, do I still need ia32-libs. When I searched > > "synaptic package manager" for ia32-libs I dont see any thing to > > install. > > Axel no longer provides 32-bit binaries of CNS 1.3. It sounds like you have > your cns_solve_env file set up correctly, so now you have to install > gfortran and build a 32-bit CNS to use. > > You don't need ia32-libs on a 32-bit system. > > -ben > > -- > | Ben Eisenbraun > | SBGrid Consortium | http://sbgrid.org | > | Harvard Medical School | http://hms.harvard.edu |
Re: [ccp4bb] CNS installation
You won't have ia32-libs on a 32-bit OS - they provide libraries needed to run 32-bit applications on a 64-bit system. I doubt that reverse is even possible, so as Ben said, you'd have to compile the binaries yourself. > > Hello Ed, I have is 32 bit pc, do I still need ia32-libs. When I searched > "synaptic package manager" for ia32-libs I dont see any thing to install. > > Date: Sat, 28 Jul 2012 16:39:07 -0400 > From: epozh...@umaryland.edu > Subject: Re: [ccp4bb] CNS installation > To: CCP4BB@JISCMAIL.AC.UK > > Rajesh, > > this might be 32-vs-64 bit issue. Make sure that > you are using correct binaries. Installing ia32-libs may also > help. > > Ed. > >> >> Dear All, >> >> I am trying to install CNS in ubuntu 10.04 LTS. Even after reading > all the >> advice on CNS installation on CCP4bb, I have failed to > get it working. >> Both in bash and tcsh, cns_web works but > cns_solve gives error "command >> not found". >> > >> yogesha@yogesha-laptop:~/work$ echo $CNS_SOLVE >> >> >> /home/yogesha/sware/CNS/cns_solve_1.3 >> >> >> yogesha@yogesha-laptop:~/work$ cns_solve >> >> >> cns_solve: command not found >> >> I > don't know how to trouble shoot. >> Any help is appreciated. >> >> Thanks >> Yogi >> > > > -- > Edwin Pozharski, PhD > University of Maryland, Baltimore -- Edwin Pozharski, PhD University of Maryland, Baltimore
Re: [ccp4bb] CNS installation
Hi Rajesh, > Hello Ed, I have is 32 bit pc, do I still need ia32-libs. When I searched > "synaptic package manager" for ia32-libs I dont see any thing to > install. Axel no longer provides 32-bit binaries of CNS 1.3. It sounds like you have your cns_solve_env file set up correctly, so now you have to install gfortran and build a 32-bit CNS to use. You don't need ia32-libs on a 32-bit system. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Re: [ccp4bb] CNS installation
Hello Ed, I have is 32 bit pc, do I still need ia32-libs. When I searched "synaptic package manager" for ia32-libs I dont see any thing to install. Date: Sat, 28 Jul 2012 16:39:07 -0400 From: epozh...@umaryland.edu Subject: Re: [ccp4bb] CNS installation To: CCP4BB@JISCMAIL.AC.UK Rajesh, this might be 32-vs-64 bit issue. Make sure that you are using correct binaries. Installing ia32-libs may also help. Ed. > > Dear All, > > I am trying to install CNS in ubuntu 10.04 LTS. Even after reading all the > advice on CNS installation on CCP4bb, I have failed to get it working. > Both in bash and tcsh, cns_web works but cns_solve gives error "command > not found". > > yogesha@yogesha-laptop:~/work$ echo $CNS_SOLVE > > > /home/yogesha/sware/CNS/cns_solve_1.3 > > > yogesha@yogesha-laptop:~/work$ cns_solve > > > cns_solve: command not found > > I don't know how to trouble shoot. > Any help is appreciated. > > Thanks > Yogi > -- Edwin Pozharski, PhD University of Maryland, Baltimore
Re: [ccp4bb] CNS installation
Rajesh, this might be 32-vs-64 bit issue. Make sure that you are using correct binaries. Installing ia32-libs may also help. Ed. > > Dear All, > > I am trying to install CNS in ubuntu 10.04 LTS. Even after reading all the > advice on CNS installation on CCP4bb, I have failed to get it working. > Both in bash and tcsh, cns_web works but cns_solve gives error "command > not found". > > yogesha@yogesha-laptop:~/work$ echo $CNS_SOLVE > > > /home/yogesha/sware/CNS/cns_solve_1.3 > > > yogesha@yogesha-laptop:~/work$ cns_solve > > > cns_solve: command not found > > I don't know how to trouble shoot. > Any help is appreciated. > > Thanks > Yogi > -- Edwin Pozharski, PhD University of Maryland, Baltimore
Re: [ccp4bb] CNS installation
Yes, I did. in bash shell, .bashrc has "source /home/yogesha/sware/CNS/cns_solve_1.3/.cns_solve_env_sh", I guess it does same thing you are suggesting. in tcsh, .tcshrc has "source /home/yogesha/sware/CNS/cns_solve_1.3/cns_solve_env" and I source .tcshrc from my work directory cns_solve_env has "setenv CNS_SOLVE '/home/yogesha/sware/CNS/cns_solve_1.3/' " .cns_solve_env_sh has "CNS_SOLVE=/home/yogesha/sware/CNS/cns_solve_1.3" I am not sure what is missing. Thanks Yogi Date: Sat, 28 Jul 2012 14:51:38 -0400 From: rrowl...@colgate.edu To: ccp4...@hotmail.com Subject: Re: [ccp4bb] CNS installation Have you sourced the CNS evironment variable file? For example, on my student workstations, we have an alias 'cnssetup' that invokes the command 'source /usr/local/xtal/cns_solve_1.3/cns_solve_env'. The source command has to be run every time a new terminal window is opened to set the paths to the executables. Cheers, Roger Rowlett On 07/28/2012 12:40 PM, Rajesh Kumar wrote: Dear All, I am trying to install CNS in ubuntu 10.04 LTS. Even after reading all the advice on CNS installation on CCP4bb, I have failed to get it working. Both in bash and tcsh, cns_web works but cns_solve gives error "command not found". yogesha@yogesha-laptop:~/work$ echo $CNS_SOLVE /home/yogesha/sware/CNS/cns_solve_1.3 yogesha@yogesha-laptop:~/work$ cns_solve cns_solve: command not found I don't know how to trouble shoot. Any help is appreciated. Thanks Yogi
[ccp4bb] CNS installation
Dear All, I am trying to install CNS in ubuntu 10.04 LTS. Even after reading all the advice on CNS installation on CCP4bb, I have failed to get it working. Both in bash and tcsh, cns_web works but cns_solve gives error "command not found". yogesha@yogesha-laptop:~/work$ echo $CNS_SOLVE /home/yogesha/sware/CNS/cns_solve_1.3 yogesha@yogesha-laptop:~/work$ cns_solve cns_solve: command not found I don't know how to trouble shoot. Any help is appreciated. Thanks Yogi
Re: [ccp4bb] CNS installation
Dear ccp4 users, I succeeded to install and use CNS 1.3 on 64bit Debain-based Linux distributions. Here my report: 1. install CNS and edit cns_solve_env as described by http://cns-online.org/v1.3/; 2. no other modifications of cns_solve_env or .cns_solve_ens_sh were required; use only the first script; 3. in a shell, move to the directory you want to work in and type /CNS_intsallation_dir/cns_solve_1.3/cns_solve_env: this will set all environment variables for that shell (remember to work only on it - csh or tcsh is required, if not present, install one); 4. in the same shell, type cns_solve; 5. the CNS prompt will appear; 6. now, it is possible to run any .inp just typing @command (i.e. CNSsolve>@cross_rotation.inp). cns_solve_env and cns_solve_env_sh do not run if I stay in the installation directory; that is, running them in ~/xtal/CNS/cns_solve_1.3 I still receive the message "Word too long". I don't know why That's all. So far, CNS runs both under Ubuntu 12.04 and Debian 6.0.4. Thanks to all for precedent replies. Best regards Fulvio Saccoccia Dept. of Biochemical Sciences Sapienza University of Rome, Italy
Re: [ccp4bb] CNS installation
I think the bash-compatible startup script has disappeared from CNS
distribution at some point. The one that was distributed with cns 1.1
still works though, and I attach my copy of it.
On 07/12/2012 11:24 AM, Dirk Kostrewa wrote:
Dear Fulvio Saccoccia,
along the lines of Ian Tickle's reply: there should be a script
"cns_solve_env_sh" using /bin/sh, which is usually a soft-link to
/bin/bash. I use this script for setup of CNS under bash.
Best regards,
Dirk.
Am 12.07.12 16:49, schrieb fulvio saccoccia:
Dear ccp4 users,
I tried to install CNS under Debian 64bit. I followed the
installation
giude as reported by CNS developers but I received the following
message when souurcing cns_solve_env:
bash: setenv: command not found
bash: setenv: command not found
bash: cns_solve_env: line 32: syntax error near unexpected token
`setenv'
bash: cns_solve_env: line 32: ` if ( ! $?CNS_ARCH ) setenv CNS_ARCH `
$CNS_SOLVE/bin/getarch`'
I know that the script would set all variables; it is indicated for csh
(or tcsh) shell. I tried to run the script under a csh shell but I
received a different error:
Word too long
The above statement is also received if a bash-optimized script is run.
Does anyone have experience in CNS installation and environment setting?
Any advice?
Thanks in advance
Fulvio Saccoccia
Dept. of Biochemical Sciences
Sapienza University of Rome, Italy
#!/bin/sh
#
# This file sets up the appropriate environmental variables and paths
# for CNSsolve. In the case of the same machines with different versions
# of the OS, backward compatibility is assumed - ie. a later version will
# be setup for a previous version of the OS if nothing else is available.
#
# written by: Paul Adams
#
# copyright Yale University
#
# ==
#
# >> Important: define the location of the CNSsolve directory <<
#
# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY
CNS_SOLVE='/sware/cns'
#
# ==
#
# full expansion of the CNS_SOLVE variable prior to use.
#
export CNS_SOLVE; CNS_SOLVE=$CNS_SOLVE
#
# ==
#
# set the number of threads for SGI multiprocessors
# if this causes a problem on other systems it can be commented out
#
export MP_SET_NUMTHREADS; MP_SET_NUMTHREADS=1
#
# ==
#
# get the machine architecture
#
if [ -d $CNS_SOLVE ]; then
if [ ! "$CNS_ARCH" ]; then
export CNS_ARCH; CNS_ARCH=`$CNS_SOLVE/bin/getarch`
fi
else
export CNS_ARCH; CNS_ARCH='unknown'
fi
#
# ==
#
# general environmental variables
#
export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries
export CNS_MODULE; CNS_MODULE=$CNS_SOLVE/modules
export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar
export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb
export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal
export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr
export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray
export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal
export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr
export CNS_HELPLIB; CNS_HELPLIB=$CNS_SOLVE/helplib
#
# general user aliases
#
cns_web () { $CNS_SOLVE/bin/cns_web; }
cns_header () { $CNS_SOLVE/bin/cns_header; }
cns_info () { cat $CNS_SOLVE/bin/cns_info; }
cns_transfer () { $CNS_SOLVE/bin/cns_transfer; }
if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then
cns_edit () { $CNS_SOLVE/bin/cns_edit_local; }
else
cns_edit () { $CNS_SOLVE/bin/cns_edit; }
fi
run_tutorial () { "csh -f tutorial.csh"; }
#
# g77 compilation and use
#
g77on () { CNS_G77=ON; . $CNS_SOLVE/.cns_solve_env_sh; }
g77off () { unset CNS_G77; . $CNS_SOLVE/.cns_solve_env_sh; }
#
# developer aliases
#
run_tests () { $CNS_SOLVE/bin/run_tests; }
run_diffs () { $CNS_SOLVE/bin/run_diffs; }
maketar () { $CNS_SOLVE/bin/maketar; }
create_patch () { $CNS_SOLVE/bin/create_patch; }
#
#
# ==
#
# to do expansions - unset noglob just in case user has it otherwise
#
set +f
#
# try to set up appropriate path
#
# first strip off any trailing information (eg. _g77)
#
CNS_ARCH=`echo ${CNS_ARCH} | sed -e 's/_g77//g'`
#
cns_vendor=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $1}'`
cns_cpu=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $2}'`
cns_os=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $3}'`
cns_major=`echo $CNS_ARCH | awk 'BEGIN{FS="-"}{print $4}'`
cns_minor=`echo $cns_major | sed -e 's/\./ /g'`
#
# if we are looking for a specific type of setup then limit search
#
cns_dirs=""
if [ ! "$CNS_G77" ]; then
if /bin/ls -d $CNS_SOLVE/$cns_vendor-* >/dev/null 2>&1 ; then
cns_dirs="`/bin/ls -d $CNS_SOLVE/$cns_vendor-* 2>&1 | awk
'BEGIN{FS="/"}{print $NF}' | sort -t\- +3 -4 -n -r`"
fi
else
CNS_ARCH="${CNS_ARCH}_g77"
if /bi
Re: [ccp4bb] CNS installation
Dear Fulvio Saccoccia, along the lines of Ian Tickle's reply: there should be a script "cns_solve_env_sh" using /bin/sh, which is usually a soft-link to /bin/bash. I use this script for setup of CNS under bash. Best regards, Dirk. Am 12.07.12 16:49, schrieb fulvio saccoccia: Dear ccp4 users, I tried to install CNS under Debian 64bit. I followed the installation giude as reported by CNS developers but I received the following message when souurcing cns_solve_env: bash: setenv: command not found bash: setenv: command not found bash: cns_solve_env: line 32: syntax error near unexpected token `setenv' bash: cns_solve_env: line 32: ` if ( ! $?CNS_ARCH ) setenv CNS_ARCH ` $CNS_SOLVE/bin/getarch`' I know that the script would set all variables; it is indicated for csh (or tcsh) shell. I tried to run the script under a csh shell but I received a different error: Word too long The above statement is also received if a bash-optimized script is run. Does anyone have experience in CNS installation and environment setting? Any advice? Thanks in advance Fulvio Saccoccia Dept. of Biochemical Sciences Sapienza University of Rome, Italy -- *** Dirk Kostrewa Gene Center Munich Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] CNS installation
Hi Fulvio Your scripts are for csh (or tcsh) so won't work under bash. Have you checked whether there are versions for sh (or bash) already set up? If not you will have to run them under csh, or better still tcsh. If the script doesn't work with the version of csh or tcsh you are using you should try debugging it, since the error message by itself is fairly useless without knowing which command in your script caused it. Debugging shell scripts is very simple: just type 'set verbose' or 'set echo' at the command line before sourcing your script: 'set verbose' echoes the lines of your script before variable substitution, and 'set echo' echoes them after substitution (the 'unset' command reverses the effect of 'set'). You should be able to tell from the last line echoed which is the offending command in the script that is giving the error message; then we can go from there. An unfortunate downside of using csh/tcsh is that unlike bash the syntax is not standardised, so if despite all efforts at debugging, the version you are using steadfastly refuses to work, you could try to install another version, though admittedly this may not be easy if it's not supported by your distribution. Cheers -- Ian On 12 July 2012 15:49, fulvio saccoccia wrote: > Dear ccp4 users, > I tried to install CNS under Debian 64bit. I followed the installation > giude as reported by CNS developers but I received the following > message when souurcing cns_solve_env: > > bash: setenv: command not found > bash: setenv: command not found > bash: cns_solve_env: line 32: syntax error near unexpected token > `setenv' > bash: cns_solve_env: line 32: ` if ( ! $?CNS_ARCH ) setenv CNS_ARCH ` > $CNS_SOLVE/bin/getarch`' > > I know that the script would set all variables; it is indicated for csh > (or tcsh) shell. I tried to run the script under a csh shell but I > received a different error: > > Word too long > > The above statement is also received if a bash-optimized script is run. > > Does anyone have experience in CNS installation and environment setting? > Any advice? > > Thanks in advance > > Fulvio Saccoccia > Dept. of Biochemical Sciences > Sapienza University of Rome, Italy
[ccp4bb] CNS installation
Dear ccp4 users, I tried to install CNS under Debian 64bit. I followed the installation giude as reported by CNS developers but I received the following message when souurcing cns_solve_env: bash: setenv: command not found bash: setenv: command not found bash: cns_solve_env: line 32: syntax error near unexpected token `setenv' bash: cns_solve_env: line 32: ` if ( ! $?CNS_ARCH ) setenv CNS_ARCH ` $CNS_SOLVE/bin/getarch`' I know that the script would set all variables; it is indicated for csh (or tcsh) shell. I tried to run the script under a csh shell but I received a different error: Word too long The above statement is also received if a bash-optimized script is run. Does anyone have experience in CNS installation and environment setting? Any advice? Thanks in advance Fulvio Saccoccia Dept. of Biochemical Sciences Sapienza University of Rome, Italy
