RE: AMBER: solutions of amber installation problems

From: Ross Walker <>
Date: Tue, 14 Jun 2005 21:55:20 -0700

Let me add a few extra 2 cents here.
This issue is due to the difference between DOS format and UNIX format text
In a dos format txt file each line is appended with a Line Feed (ASCII code
10) and a Carriage Return (ASCII code 13).
In comparison a Unix format text file has only the Line Feed.
Hence if you open a dos formatted text file on a unix machine with an editor
such as "vi" you will "^M"'s on the end of each line. These are the "stray"
carriage return characters that unix doesn't know what to do with.
Conversely if you open a unix format text file in Windows with something
like Notepad you see all the text on one line with little "squares" where
the new lines should be. This is because notepad expects to see a line feed
AND a carriage return together and so doesn't know what to do if it sees
just a line feed.
These two differing formats can cause problems when used on the wrong
machines. There are, however, a number of solutions. One option is to use
the ASCII mode when ftping files. This works by stripping the 8th bit from
each byte so reducing the text to 128 character ascii. The ftp client then
appends the correct end of line characters. However, this doesn't always
work and it certainly doesn't work if you use windows shares (samba) to copy
I find that the best option is to ALWAYS transfer files in binary mode, this
way you get the full file with no conversion. In unix you can convert from
dos to unix format using the utility DOS2UNIX or back again with the utility
UNIX2DOS. This is generally installed by default on Linux machines and I
believe the source code is available for compiling on other unix's.
When dealing with text files in windows I would start by throwing away
Microsoft's hopelessly inadequate notepad and get hold of a decent text
editor such as Textpad ( which can both read, write and
convert DOS and UNIX format text files. Alternatively and probably the best
option in when dealing with AMBER files in Windows is to install the Bash
shell for Windows (AKA Cygwin - and then stick entirely with
UNIX format text files. In this way you can avoid confusion over what format
your text file is in / should be in.
Note: cygwin also comes with the DOS2UNIX and UNIX2DOS commands.
As for Gaussian input files not working with the auto select option in FTP I
assume this is due to # and % symbols that may be confusing the ftp client's
"text detection routine". Stick to always using binary format and doing the
conversion manually yourself and you will have a lot less headaches.
All the best
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- |
| | PGP Key available on request |

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From: [] On Behalf Of
Zhang Bing
Sent: 14 June 2005 19:42
Subject: AMBER: solutions of amber installation problems

Dear all:


About two weeks ago, I published my amber installation problems here. Now,
they have been resolved and I put our solution here, you can refer to it if
you have the same problems.


Actually, it is not because of the MPI, the machine or something else, the
reason is the file transfer mode. We only changed the file transfer mode
from Auto select to ASCII and then everything was OK. When we upload or
download files between our PCs and the clusters, we have to use the SSH
Secure File Transfer tool (or some other tools), the Operation/File Transfer
Mode manual item can help us to select the mode we need. The default option
is "Auto select" and in most of the transfers I know, it is no need to
change it, except for Gaussian (a classic Quantum Chemistry application)
input files. I don't know why.


PS. If we upload a Gaussian input file written in txt format with an Auto
Select mode, then in Linux, at the end of each line, there is a strange
symbol "^M" in light grey.


The following is two former letters I issued:


Dear all:


We are trying to install Amber8 on our PC-cluster with athlon platform,
MPICH and compiler ifort and have finished the compiling works; however,
when testing parallel works, something very strange happened. I issue the
steps of compiling and problems in my test works here:


Setenv AMBERHOME /user/local/amber8


Setenv MPICH_HOME /user/local...


../configure -athlon -static ifort


Make serial


Make test.<programme-name>


Make clean


../configure -mpich -static ifort


Make parallel


At the end of the compiling, the machine told me everything was ok and the
single threaded works passed the test smoothly. But when I did these:




Setenv DO_PARALLEL "mpirun -np 4" (or "/user/local/mpich_ifc/bin/mpirun -np


Make test.parallel


The machine told me like this:


[nnizb.nemo test]$ make test.parallel

make: *** No rule to make target `test.parallel'. Stop.


When I test one of my works, I issued command like these:


[nnizb.nemo test]$ mpirun -np 4 sander -O -i -p 888.parm -c 888.crd
-o 888.out -r 888.rst




[nnizb.nemo test]$ /user/local/mpich_ifc/bin/mpirun -np 4 sander -O -i -p 888.parm -c 888.crd -o 888.out -r 888.rst

And the error messages were given like:


[0] MPI Abort by user Aborting program !

[0] Aborting program!

p0_12768: p4_error: : 1

Killed by signal 2.

Killed by signal 2.

Killed by signal 2.



Our OS is npaci rocks 3.3 linux (it is based on Redhat linux and very very
similar with Redhat linux).



We also failed when we tried to install amber8 on another cluster. The
administrator told us that was due to the lack of MPI library on each node,
so he has to install the library on each node. Is this true? Do you need to
do this before you install amber on your machine?



Thank you!


Zhang Bing


National University of Singapore

Nanoscience and Nanotechnology Initiative



Dear all:


I got the test jobs passed by issuing the new test command. However, when I
tried my own works, it failed again:


[nnizb.nemo exe]$ mpirun -np 4 sander -O -i -p cdk5.parm -c cdk5.crd
-o cdk.out -r cdk.rst

[0] MPI Abort by user Aborting program !

[0] Aborting program!

p0_3517: p4_error: : 1

Killed by signal 2.

Killed by signal 2.

Killed by signal 2.


I think it is something wrong with my command line. 'Coz I did see 4
processors running there simultaneously after I submitted test jobs by "make
test.sander". So now, I am wondering how you made your script for the
parallel sander and why you need a DO_PARALLEL environment variable first. I
tried to set such a variable before my "mpirun -np 4 sander -O -i -p
cdk5.parm -c cdk5.crd -o cdk.out -r cdk.rst" command, it did not work. So
would you kindly show me the script or the command line for a parallel
sander? Any advice from you will be greatly appreciated.


Sincerely yours,


Zhang Bing





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Received on Wed Jun 15 2005 - 06:53:00 PDT
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