|
| From: | Nairhita Samanta |
| Subject: | Re: [ESPResSo-users] Problem regarding Tcl; Advice: Install Linux |
| Date: | Thu, 26 Feb 2015 10:05:49 +0530 |
Dear Nairhita,
I would suggest using the following three options rather than using Cygwin
(the problems with Cygwin will only accelerate). The following list is in
increasing order of complexity:
1. Download Virtual box/ VmWare or if you are in windows 8+ activate HyperV.
Then get download iso of Ubuntu 14.04 from official site. And create a
virtual Operating system in windows.
2. Download Ubuntu iso. Mount it, find wubi copy it in the folder where you
have kept iso of Ubuntu and install wubi. Before installing make sure you
create a separate NTFS partition for installing This.
3. download iso of Ubuntu, Live Linux creator tool and make a bootable USB
of Ubuntu. Restart your computer and boot from his usb and install the
Ubuntu. Make sure you preserve your windows (read online tutorial for this
as this can lead to permanent data loss)(Don't do this on lab computer!)
How do I know this? Because like you a month ago I also started from scratch
and tried all the above.
Once you have a working copy of Linux install the following things
preferable in the same order: Tcl, Tk, FFTW, MPI/OMPI, CUDA (If
supported/required), Espresso3.3.0.
If you have any other problem reply.
Regards
Harmanjit Singh
IIT Kanpur Alumnus (BTech-2014 Batch)
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Today's Topics:
1. Error while executing mbtools package example script
(Evyatar Arad)
2. Problem in installing tcl (Nairhita Samanta)
3. Re: Problem in installing tcl (Pierre de Buyl)
4. Re: Problem in installing tcl (Pierre de Buyl)
----------------------------------------------------------------------
Message: 1
Date: Wed, 25 Feb 2015 14:09:04 +0200
From: Evyatar Arad <address@hidden>
To: address@hidden
Subject: [ESPResSo-users] Error while executing mbtools package
example script
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="utf-8"
Hello everyone,
I'm an undergrad and as a part of my final project I need to simulate Cooke
and Deserno's model for self assembling bilayer membranes (2005). I've been
trying to get the example script for simple bilayer membrane in the mbtools
package to run and received the following error.
In the documentation it stated that the example simulation script should
work right 'out of the box'...
Any idea as to what causes this?
Thanks so much in advance,
Evyatar Arad.
:: > loaded version 1.0.0 of analysis
:: > loaded version 1.3.3 of cmdline
:: > loaded version 1.0.0 of system_generation
:: > using paramsfile: simplebilayer.tcl
:: > loading parameter file .. done
::mbtools::utils > Warning: no checkpoint named
./simplebilayer//checkpoint.latest.gz
::mbtools::utils > setting up ./simplebilayer/ for simplebilayer.tcl
::mbtools::utils > set interaction: 0 FENE 30 1.5 ::mbtools::utils > set
interaction: 1 harmonic 10.0 4.0 ::mbtools::utils > set interaction: 0 0
lennard-jones 1.0 0.95 1.066375
0.25 0.0
::mbtools::utils > set interaction: 0 1 lennard-jones 1.0 0.95 1.066375
0.25 0.0
::mbtools::utils > set interaction: 0 2 lennard-jones 1.0 0.95 1.066375
0.25 0.0
::mbtools::utils > set interaction: 1 1 lj-cos2 1.0 1.0 0.0 1.6
::mbtools::utils > set interaction: 1 2 lj-cos2 1.0 1.0 0.0 1.6
::mbtools::utils > set interaction: 2 2 lj-cos2 1.0 1.0 0.0 1.6
::mbtools::system_generation > setting up system
::mbtools::system_generation > creating a topology for moltype 0
::mbtools::system_generation::flat > placing lipids in a flat bilayer
::mbtools::system_generation > Warning: no trappedmols defined
::mbtools::utils > Setting the random seed to clock in seconds: 356729693
::mbtools::utils > initializing vmd to : offline
:: > warming up at 1.1
::mbtools::utils > warming up 20 times 100 timesteps ::mbtools::utils >
wrote file ./simplebilayer//warm.0000.gz ::mbtools::utils > run 0 of 20 at
time=0.20000000000000015 (cap=54.75) ::mbtools::utils > run 1 of 20 at
time=0.4000000000000003 (cap=104.5) ::mbtools::utils > run 2 of 20 at
time=0.6000000000000004 (cap=154.25) ::mbtools::utils > run 3 of 20 at
time=0.8000000000000006 (cap=204.0) ::mbtools::utils > run 4 of 20 at
time=1.0000000000000007 (cap=253.75) ::mbtools::utils > run 5 of 20 at
time=1.2000000000000008 (cap=303.5) ::mbtools::utils > run 6 of 20 at
time=1.400000000000001 (cap=353.25) ::mbtools::utils > run 7 of 20 at
time=1.6000000000000012 (cap=403.0) ::mbtools::utils > run 8 of 20 at
time=1.8000000000000014 (cap=452.75) ::mbtools::utils > run 9 of 20 at
time=2.0000000000000013 (cap=502.5) ::mbtools::utils > wrote file
./simplebilayer//warm.0001.gz ::mbtools::utils > run 10 of 20 at
time=2.1999999999999793 (cap=552.25) ::mbtools::utils > run 11 of 20 at
time=2.3999999999999573 (cap=602.0) ::mbtools::utils > run 12 of 20 at
time=2.5999999999999353 (cap=651.75) ::mbtools::utils > run 13 of 20 at
time=2.7999999999999132 (cap=701.5) ::mbtools::utils > run 14 of 20 at
time=2.999999999999891 (cap=751.25) ::mbtools::utils > run 15 of 20 at
time=3.199999999999869 (cap=801.0) ::mbtools::utils > run 16 of 20 at
time=3.399999999999847 (cap=850.75) ::mbtools::utils > run 17 of 20 at
time=3.599999999999825 (cap=900.5) ::mbtools::utils > run 18 of 20 at
time=3.799999999999803 (cap=950.25) ::mbtools::utils > run 19 of 20 at
time=3.999999999999781 (cap=1000.0) ::mbtools::utils > uncapping forces
::mbtools::system_generation > Warning: no user fixed particles defined
:: > warming up again at 1.1
::mbtools::utils > warming up 1 times 0 timesteps ::mbtools::utils >
Warning: warmup steps are zero
:: > starting integration: run 100 times 100 steps ::mbtools::analysis >
setting up analysis The operation "get_lipid_orients" you requested is not
implemented.
while executing
"analyze get_lipid_orients "
(procedure "setup_flipflop" line 30)
invoked from within
"setup_flipflop"
("eval" body line 1)
invoked from within
"eval $setupcommand"
(procedure "::mbtools::analysis::setup_analysis" line 61)
invoked from within
"::mbtools::analysis::setup_analysis $analysis_flags -outputdir $outputdir
-g $mgrid -str $stray_cut_off"
(file "./scripts/main.tcl" line 236)
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Message: 2
Date: Wed, 25 Feb 2015 19:15:31 +0530
From: Nairhita Samanta <address@hidden>
To: address@hidden
Subject: [ESPResSo-users] Problem in installing tcl
Message-ID:
<CAO5MpDdjfT8sQ_PpsUNBp5mk1rqSCs5KtJZpi9HrV=address@hidden>
Content-Type: text/plain; charset="iso-8859-1"
Hi everyone!
I am a new user and right now in the installation phase.
I have been able to install fftw, but when I am trying to install tcl, I am
getting this following error message after giving the command "make"
"i686-w64-mingw32-gcc -c -O2 -fomit-frame-pointer -Wall -I"./../generic"
-DTCL_TOMMATH -DMP_PREC=4 -I"./../libtommath" -I"." -pipe
-DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
-DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1
-DTCL_CFGVAL_ENCODING=\"cp1252\" -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1
-DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_NO_SEH=1
-DEXCEPTION_DISPOSITION=int -DHAVE_NO_FINDEX_ENUMS=1 -DNDEBUG=1
-DTCL_CFG_OPTIMIZED=1 -DBUILD_tcl "./../generic/regcomp.c" -o regcomp.o
/bin/sh: i686-w64-mingw32-gcc: command not found
make: *** [regcomp.o] Error 127"
I have tried version tcl8517-src.zip and Can anyone help me out of this
situation? As I think I cannot install Espresso without installing this.
Thank and regards,
Nairhita Samanta
Ph.D student
IIT Bombay
Mumbai, India
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Message: 3
Date: Wed, 25 Feb 2015 14:51:35 +0100
From: Pierre de Buyl <address@hidden>
To: address@hidden
Subject: Re: [ESPResSo-users] Problem in installing tcl
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii
On Wed, Feb 25, 2015 at 07:15:31PM +0530, Nairhita Samanta wrote:
> Hi everyone!
> I am a new user and right now in the installation
> phase. I have been able to install fftw, but when I am trying to
> install tcl, I am getting this following error message after giving
> the command "make"
> "i686-w64-mingw32-gcc -c -O2 -fomit-frame-pointer -Wall
> -I"./../generic" -DTCL_TOMMATH -DMP_PREC=4 -I"./../libtommath" -I"."
> -pipe -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1
> -DTCL_CFGVAL_ENCODING=\"cp1252\" -DHAVE_SYS_TYPES_H=1
> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_NO_SEH=1
> -DEXCEPTION_DISPOSITION=int -DHAVE_NO_FINDEX_ENUMS=1 -DNDEBUG=1
> -DTCL_CFG_OPTIMIZED=1 -DBUILD_tcl "./../generic/regcomp.c" -o
> regcomp.o
> /bin/sh: i686-w64-mingw32-gcc: command not found
> make: *** [regcomp.o] Error 127"
Also, it seems that cygwin includes tcl so that is your first step.
http://wiki.tcl.tk/1866
> I have tried version tcl8517-src.zip and Can anyone help me out of
> this situation? As I think I cannot install Espresso without
> installing this.
> Thank and regards,
> Nairhita Samanta
> Ph.D student
> IIT Bombay
> Mumbai, India
--
-----------------------------------------------------------
Pierre de Buyl
KU Leuven - Institute for Theoretical Physics T +32 16 3 27355 W
http://pdebuyl.be/
-----------------------------------------------------------
------------------------------
Message: 4
Date: Wed, 25 Feb 2015 14:50:12 +0100
From: Pierre de Buyl <address@hidden>
To: address@hidden
Subject: Re: [ESPResSo-users] Problem in installing tcl
Message-ID: <address@hidden>
Content-Type: text/plain; charset=us-ascii
On Wed, Feb 25, 2015 at 07:15:31PM +0530, Nairhita Samanta wrote:
> Hi everyone!
> I am a new user and right now in the installation
> phase. I have been able to install fftw, but when I am trying to
> install tcl, I am getting this following error message after giving the
> command "make"
> "i686-w64-mingw32-gcc -c -O2 -fomit-frame-pointer -Wall
> -I"./../generic" -DTCL_TOMMATH -DMP_PREC=4 -I"./../libtommath" -I"."
> -pipe -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\"
> -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1
> -DTCL_CFGVAL_ENCODING=\"cp1252\" -DHAVE_SYS_TYPES_H=1
> -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
> -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
> -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_NO_SEH=1
> -DEXCEPTION_DISPOSITION=int -DHAVE_NO_FINDEX_ENUMS=1 -DNDEBUG=1
> -DTCL_CFG_OPTIMIZED=1 -DBUILD_tcl "./../generic/regcomp.c" -o
> regcomp.o
> /bin/sh: i686-w64-mingw32-gcc: command not found
> make: *** [regcomp.o] Error 127"
> I have tried version tcl8517-src.zip and Can anyone help me out of this
> situation? As I think I cannot install Espresso without installing
> this.
Do you have a C compiler installed? "i686-w64-mingw32-gcc" means that the
compiler "i686-w64-mingw32-gcc" is not found. I am not familiar with windows
and
cygwin but a working installation with a C and C++ compiler is needed for
what
you want to do.
Pierre
------------------------------
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