Re: [plumed-users] patching plumed-1.3 with NAMD

[Giovanni Bussi]

Dear Francesco,

in principle you should revert the patch, but the revert system is not super-robust. Moreover, since the patch failed, I am not sure you can revert it properly.

I suggest you to start from scratch!

Regards,

Giovanni

On Thu, Mar 7, 2013 at 6:20 PM, <chien...@gmail.com> wrote:

Hello:
I first patched plumed-1.3 without having properly configured NAMD (whereby I did not get a NAMD building directory).

Therefore. patching was not completed:

* I will try to patch PLUMED version 1.3 ...
-- Executing pre script
-- Setting up symlinks
-- Setting up recon symlinks
-- Applying patches
patching file ./src/SimParameters.h
Hunk #1 succeeded at 432 (offset 92 lines).
patching file ./src/SimParameters.C
Hunk #1 succeeded at 1439 (offset 98 lines).
Hunk #3 succeeded at 4350 (offset 196 lines).
patching file ./src/ComputeMgr.C
Hunk #1 succeeded at 82 with fuzz 1 (offset 10 lines).
Hunk #2 succeeded at 790 (offset 178 lines).
patching file ./Makefile
Hunk #2 succeeded at 172 with fuzz 1 (offset 32 lines).
Hunk #3 succeeded at 356 with fuzz 1 (offset 50 lines).
Hunk #4 succeeded at 403 with fuzz 3 (offset 51 lines).
Hunk #5 succeeded at 429 (offset 53 lines).
-- Executing post script
./plumedpatch_namd.sh: line 70: cd: Linux-x86_64-g++: No such file or directory
Makefile:10: Make.config: No such file or directory
plumed.inc:39: *** missing separator.  Stop.
- DONE!

Then, I correctly configured NAMD, getting a valid building directory. Following that, I re-run the patching script, which proved unable to find the line

source $plumedir/patches/patch_tool.sh

although "echo $plumedir" showed that plumedir was still available.

Question: should I redo patching from scratch, i.e., deleting everything done previously to this regard, while saving the NAMD building directory? Or can the patching be completed "by hand"?

Thanks
francesco pietra

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[davide branduardi]

Hi Francesco
There are a couple of things you can do.
First check if the directory that namd configuration procedure creates is

Linux-x86_64-g++

If not, enter the patch ./plumedpatch_namd.sh
and you should find a line:

# USER DEFINED ARCHITECTURE:
myarch="Linux-x86_64-g++"


set myarch to the right one.

I also suspect that anyhow your patching is already fine and what you need
to do is to enter the directory that namd config created (for the sake
of convenience
let's keep calling it Linux-x86_64-g++ ) and do

make depends

As Giovanni is saying it is better to modify the namd patch and start
from scratch again.
CiaoCiao

D
******************************************************
Davide Branduardi,
Postdoc
Theoretical Molecular Biophysics Group
Office 2.255
Max Planck Institute for Biophysics
Max-von-Laue-Straße 3
60438 Frankfurt am Main
Phone: +49 (0)69 63031503
Fax: +49 (0)69 63031502
davide.b...@biophys.mpg.de
davide.b...@gmail.com
Web:
https://sites.google.com/site/davidebranduardi
******************************************************

[chien...@gmail.com]

I could not answer Davide directly, therefore I copy his suggestions here

Hi Francesco
There are a couple of things you can do.
First check if the directory that namd configuration procedure creates is

Linux-x86_64-g++

If not, enter the patch  ./plumedpatch_namd.sh
and you should find a line:

# USER DEFINED ARCHITECTURE:
myarch="Linux-x86_64-g++"


set myarch to the right one.

I also suspect that anyhow your patching is already fine and what you need
to do is to enter the directory that namd config created (for the sake
of convenience
let's keep calling it Linux-x86_64-g++ ) and do

make depends

Hi davide:
myarch and NAMD building directory are Hi Francesco

Hi Davide
Both myarch and NAMD buiding directory were Linux-x86_64-g++. Running "make depends"
  francesco@.....:~/OLD_NAMD_2.9_Source/Linux-x86_64-g++$ make depends
Makefile:12: plumed.inc: No such file or directory
make: *** No rule to make target `plumed.inc'.  Stop.
francesco@....:~/OLD_NAMD_2.9_Source/Linux-x86_64-g++$
although Mefile contains, as first lines: # pass version/platform information to compile
NAMD_VERSION = 2.9

# compiler flags (Win32 overrides)
COPTI = -I
COPTC = -c
COPTD = -D
COPTO = -o $(SPACE)

include Make.config

include plumed.inc

# define below Make.config so Win32 can change default target to winall
default: all THIS PAGE IS CURIOUS: trying to create a line probably send a message. Should that have occurred, I beg pardon. If there is a way to recover the situation, I would be happy. Though, I am prepared to redo from scratch (in the above, NAMD building directory was created after plumed patching) Thanks, francesco

As Giovanni is saying it is better to modify the namd patch and start
from scratch again.



As Giovanni is saying it is better to modify the namd patch and start
from scratch again.

[chien...@gmail.com]

While saving this NAMD directory, in case it might turn out useful (i.e., recoverable), I restarted from scratch. I decided to try to compile NAMD with plumed although I was informed that bias exchange (which I need) is not available in this code. I'll look for other possibilities within plumed. Unfortunately, my hardware is not supported by gromacs, where bias exchange is available.

I restarted from a NAMD directory where charm++, fftw, tcl, and tcl-threaded had already been generated without errors.

plumedpatch was copied from /patches to the NAMD directory.

The env plumedir was exported.

NAMD was configured, generating a NAMD building directory that had the same name "Linux-x86_64-g++" as for
myarch in the plumedpatch.

Running the plumedpatch, errors were reported:

./plumedpatch_namd.sh: line 51: syntax error near unexpected token `('
./plumedpatch_namd.sh: line 51: `      echo -n "    \$(DSTDIR)/${f%.c}.o"'


Line 51 and surrounding lines of the plumedpatch are shown below:

echo -n "PLUMED_OBJECTS="
    for file in $plumedir/common_files/*.c
      do f=${file##*/}
      echo "    \\"
      echo -n " \$(DSTDIR)/${f%.c}.o"       (LINE 51)
    done
    echo
    if [ "$RECON_LIBS" != "" ] ; then
      for file in $plumedir/recon_src/*.cpp
        do f=${file##*/}
        echo "  \\"
        echo -n " \$(DSTDIR)/${f%.cpp}.o"

I am unable to detect my mistake. No good excuse, I admit. Though, while trying to correct myself, I rely on your kind advice.


Thanks

francesco

[chien...@gmail.com]

I made some progress, though not to final success. Therefore, please disregard this the message below. I have first to contact Davive before posting what occurred.
Thanks
francesco