Re: [ccp4bb] problems about installation of mosflm701

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CCP4bb <-- 2008 <-- March 2008 <-- 27 March 2008

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Subject: Incubator for Crystallization plates
From: Orly Dym orly {- dot -} dym {- at -} WEIZMANN {- dot -} AC {- dot -} IL
Date: 2008-03-27

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Subject: Re: problems about installation of mosflm701
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-03-27

Subject: Re: problems about installation of mosflm701
From: harry powell harry {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2008-03-27

Hi

First off, you really shouldn't be installing mosflm version 7.0.1 -
version 7.0.3 is the current one, and contains numerous bug fixes.
The developers are likely to meet any problem queries relating to
7.0.1 with "update to the current version first, then try again; if
the problem persists, we will look at it"...

Your immediate problem is that you are trying to run a csh script as
a bash script, without editing the file properly; e.g., you can't
just change "setenv" (csh) to "export" (bash) - the syntax is not the
same - you'd need to change it thus -

setenv CCP4_LIB_FILES '-lccp4f -lccp4c -lxdl_view'

would become something like

export CCP4_LIB_FILES='-lccp4f -lccp4c -lxdl_view'

You would also need to change the top line of the file so that it was
something like "#!/bin/bash -f", though I would be more inclined to
use a proper traditional Bourne shell for this and use "#!/bin/sh -f"
and use "set"s and "export"s throughout.

If you really want to run the script, I would use tcsh or csh, rather
than trying to modify it so that it is a bash script.

BTW, the Intel compiler setup in that file is way out of date - you'd
need to change that as well to point to current copies of the compilers.

I would be very strongly inclined to install the "mosflm_linux_suse"
pre-built executable - it should certainly work on FC5, and saves you
the trouble of trying to build it. The speedup by using an executable
compiled with the Intel compiler is probably not that great - recent
g77s and gfortrans give excellent and stable optimization!

On 27 Mar 2008, at 04:57, Lu Yongzhi wrote:

>
> ----- Original Message -----
> From: Lu Yongzhi
> To: ccp4 bb
> Sent: Wednesday, March 26, 2008 7:41 PM
> Subject: problems about installation of mosflm701
>
> Hi,
>
> My OS is fedoral core 5. I have installed ccp4-6.0.2 which include
> the mosflm 6, but I want to install mosflm7.0.1. I downloaded the
> program, but I can't install it properly. I source the file
> 'intel', the echo is (I have changed the 'setenv' to 'export'):
>
>
> bash: export: `-lccp4f -lccp4c -lxdl_view': not a valid identifier
> MOSROOT has been set to
>
> bash: export: `/index': not a valid identifier
> bash: export: `/src/dps/util': not a valid identifier
> bash: export: `/jpg': not a valid identifier
> bash: intel: line 65: syntax error: unexpected end of file
>
> could anyone can help me.
>
> the lines in the 'intel' file are:
>
> #!/bin/csh -fv
> #
> # setup shell script for the development copies of Mosflm for
> different
> # platforms.
> #
> # Common stuff first
> #
> export CCP4_LIB_FILES '-lccp4f -lccp4c -lxdl_view'
> set mosroot = ${cwd:h}
> export MOSROOT $mosroot
> echo MOSROOT has been set to $MOSROOT
> set moshome = ${cwd}
> export MOSHOME $moshome
> echo $MOSHOME
> export AR_FLAGS vru
> export DPS ${MOSHOME}
> export IND ${MOSHOME}/index
> export UTIL ${MOSHOME}/src/dps/util
> export JPG ${MOSHOME}/jpg
> # intel compiler specifics - change this to your local installation
> if ( -e /opt/intel/compiler70/ia32/bin/ifcvars.csh )then
> source /opt/intel/compiler70/ia32/bin/ifcvars.csh
> else
> echo You must either edit the file called "intel" to source
> the correct
> echo ifcvars.csh file or install both the Intel C++ and FORTRAN
> compilers
> exit
> endif
> if ( -e /opt/intel/compiler70/ia32/ifc_fudge.o )then
> export FUDGE /opt/intel/compiler70/ia32/ifc_fudge.o
> export NOFUDGE ""
> else
> export FUDGE ""
> export NOFUDGE -i_dynamic
> endif
> export DEBUG ""
> export F77 "ifc ${DEBUG}"
> export FCOMP "${F77}"
> export FC "${F77}"
> export CC "icc ${DEBUG}"
> export FLINK "${F77} ${DEBUG}"
> export FFLAGS "-O -align -w90 -cm"
> export CFLAGS "-O0 -O -DPROTOTYPE -DIFC -c -w"
> # if no "fudge.o" vide infra export LFLAGS "-Vaxlib -i_dynamic"
> export LFLAGS "-Vaxlib $NOFUDGE"
> #
> # (2) Mosflm directory
> #
> export MOSFLAGS "-O3 -align -w90 -cm"
> # export MOSFLAGS "-O3 -align -w90 -cm -prof_gen" this line for
> profiling only
> # export MOSFLAGS "-O3 -align -w90 -cm -prof_use" & change $F77
> etc to include "-ipo" flag
>
> export MCFLAGS "-O0"
> export MOSLIBS "-L${CCP4_LIB} ${CCP4_LIB_FILES} -lncurses -L/
> usr/X11R6/lib -lXt -lSM -lICE -lX11 -ldl -lpthread -lm ${FUDGE}"
> #
> # (3) CBF directories
> #
> export CBFCFLAGS "-O -DPROTOTYPE -DIFC"
> # DPS
> export VERBOSE "v"
> export UTILFLAGS "-O -DPROTOTYPE -DIFC -c -w"
> export EXTRAFLAGS "-I${UTIL} "
> export STDCFLAGS ""
>
> exit
>

Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,
Hills Road, Cambridge, CB2 2QH

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CCP4bb <-- 2008 <-- March 2008 <-- 27 March 2008

Previous message:
Subject: Incubator for Crystallization plates
From: Orly Dym orly {- dot -} dym {- at -} WEIZMANN {- dot -} AC {- dot -} IL
Date: 2008-03-27

Next message:
Subject: Re: problems about installation of mosflm701
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2008-03-27