Re: compiling NAMD failed on windows with Cygwin

From: Axel Kohlmeyer (
Date: Sat Jan 10 2009 - 09:20:44 CST

On Sat, 10 Jan 2009, accomp lin wrote:


JL> changed all "\" into "/" and the problem disappear. However, I got a
JL> new error, it says:

JL> /usr/lib/gcc-lib/i686-pc-cygwin/3.3.3/../../../..i686-pc-cygwin/bin/ld:
JL> cannot find -ltcl8.3 collect2: ld returened 1 exit status Fatal
JL> error by charmc in directory .....

JL> I already downloaded window version of TCL and fixed the path to its
JL> files as NAMD release notes states. So what's the problem. Should I

how the hell should _i_ know?? from the information that you provide
i can only extract that your linker cannot find the tcl library.

i cannot read your mind or the mind of your computer and see exactly
what you have done. there are several possible reason: typos in your
arch files, errors in the installation, incompatible libraries.

JL> copy TCL libs into some directory of Cygwin manually? Thank you

why waste you time on compiling NAMD for windows anyways??

unless you have a windows cluster with myrinet or infiniband
(...and who would even want to set up such a monstrosity?),
i don't see any reason for not using the precompiled binaries.


JL> Regards
JL> Jiaqi
JL> --- 08˙˙12˙˙29˙˙˙˙˙˙˙˙, Axel Kohlmeyer <> ˙˙˙˙˙˙
JL> ˙˙˙˙˙˙: Axel Kohlmeyer <>
JL> ˙˙˙˙: Re: namd-l: compiling NAMD failed on windows with Cygwin
JL> ˙˙˙˙˙˙: "accomp lin" <>
JL> ˙˙˙˙:
JL> ˙˙˙˙: 2008,1229,˙˙˙˙,11:36˙˙˙˙
JL> On Mon, 29 Dec 2008, accomp lin wrote:
JL> J> Dear developer of NAMD:
JL> dear jiaqi,
JL> J> I'm compiling NAMD on windows with Cygwin. I tried several time but
JL> failed. The problem is that i didn't set the directory of charm5.9, tcl,
JL> fftw in .arch file correctly. After making this right, I finally got the NAMD
JL> compling on progress. But I then I got the follows error:
JL> J>  
JL> J> -LE:\Mr.Lin\comp\NAMD_2.6_Source\tcl/lib -ltcl8.3 \
JL> J> -LE:\Mr.Lin\comp\NAMD_2.6_Source\fftw/lib -lsrfftw
JL> -lsfftw \
JL> J> obj/dcdplugin.o  \
JL> J> \
JL> J> -lm -o namd2
JL> J> E:Mr.LincomNAMD_2.6_Sourcecharm-5.9/net-Cygwin/bin/charmc: not found
JL> J> make: *** [namd2] Error 127
JL> J>  
JL> J> I browsed to the .../net-Cygwin/bin/ directory but I found a charmc
JL> J> link is actually there. So what's my problem? Is that becasue some
JL> J> "\" is lacked in the command? Where can I find the command
JL> so I can
JL> J> add the "\" to it myself?
JL> J>  
JL> J> Please help
JL> please read the cygwin documentation more carefully!
JL> cygwin emulates a unix environment, so everything you
JL> provide - for example path names - has to be giving
JL> in "unix"-format and the unix path separator is the
JL> forward slash '/'. the backward slash '\' is an escape
JL> character in scripts and makefiles and as such indicates
JL> to use the next character literally. because of that
JL> your build script cannot find the charmc script, because
JL> it is looking in the wrong location.
JL> to produce a backslash you'd have to use '\\' (or
JL> '\\\\'
JL> in case the string is interpreted twice), but i recommend
JL> to specify all paths with '/' to avoid this.
JL> cheers,
JL> axel.
JL> J> Thank you!
JL> J>  
JL> J>  
JL> J> Jiaqi
JL> J>  
JL> J>  
JL> ___________________________________________________________
JL> ˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙˙

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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