Journal on Bachelor Degree

One Problem Solved, Come Another Problem

2010-01-25T14:52:00.002+07:00

This is some solution comes from DOVIS Developer

Hi Muhammad,

It took a while but here are some suggestions.
The changes in the dovis_dock.cpp and perl scripts are not working because you are using the options for “lockfile” instead of those for “lockfile-create”.
check:
http://www.tin.org/bin/man.cgi?section=1&topic=lockfile-create
and
http://linux.about.com/library/cmd/blcmdl1_lockfile.htm

I have added below some suggestions on how to alter the code but they may not be 100% correct and you may need to include additional changes. I cannot test here because I don’t have a machine with the Debian Sarge OS.

Daniel

insert this line into dovis_dock.h
after line 47, inside the definition of DOVIS_DATA_TYPE)

std::string lock_command2;

In dovis_dock.cpp file:
Replace these three lines (lines 287-289):

command_oss.str("");
command_oss << "lockfile -" << dovis_data.lock_sleep_time;command_oss << " -r " << dovis_data.lock_retries << " ";with

command_oss.str("");
command_oss << "lockfile-touch “dovis_data.lock_command2 = command_oss.str();command_oss.str("");command_oss << "lockfile-create –retry “ << dovis_data.lock_retries << " ";-------Also, after line 475 of dovis_dock.cpp, which reads:

command_oss << dovis_data.lock_command << dovis_data.job_control_lock_1;add:

command_oss << dovis_data.lock_command2 << dovis_data.job_control_lock_1 << " & ";-----after lines 1488 and 1682 of dovis_dock.cpp, which read:

command_oss << dovis_data.lock_command << dovis_data.job_control_lock_2;add:

command_oss << dovis_data.lock_command2 << dovis_data.job_control_lock_2 << " & ";In the perl script you should include something like:

my $lockfile_command = "lockfile-create --retry " . $dovis_opt{LOCK_RETRIES};
my $lockfile_command2 = "lockfile-touch ”;

Then, after these lines:
#############################

# get lock to log cpu count

#############################
if (system "$lockfile_command $lockfile")
{
print "Can not get init lock!\n";
exit;
}

Add these ones

if (system "$lockfile_command2 $lockfile & ")
{
print "Cannot lock_touch file!\n";
exit;
}

And the result is

Well, I still have to work hard then . . . . .

Horray, I've got the solution

2010-01-15T10:43:00.000+07:00

Horray, I've got the solution for the previous problem.

Mr Daniel Ripoll personally sent it yesterday.

It seems I could work with it next tuesday.

Tommorow till monday, I've backpacking trip to Ujung Genteng, Sukabumi.

Have a nice weekend

Problems Today

2010-01-06T11:20:00.005+07:00

Dear DOVIS developer

I got trouble when trying to install DOVIS

First, I checked the lockfile command on my OS (Debian Sarge)

Yeah, the lockfile is on my OS with different form (lockfile-create)
So, I changed the dovis_dock.cpp source code from original installer (openbabel)

Before

After

I install DOVIS in the usual way
Then I changed the dovis_dock_driver.pl source code from script folder

Before

After

But, still there's some mistake on my process
The result is

Actually, I'm newbie on using DOVIS and Debian
I hope I can get some assistance on installation and running some test

Thank You

Muhammad H Hilman

Can not access hastinapura !!!

2010-01-04T08:49:00.005+07:00

Today, on my first 2010 day
When I already in front of my computer
Doing DOVIS work on hastinapura

I CAN'T ACCESS THE SERVER

updated:
It's my wrong, I forgot my username and password

Research Plan

2009-12-31T09:36:00.003+07:00

Unless he is fool than everybody need a plan
This is my plan for the research

Two weeks on January (1-15 January 2010)

Completing installation DOVIS 2.0 on hastinapura server
Doing run testing using dummy data on DOVIS 2.0

Next plan will be updated after I met my research advisor =)

The Blog is Revived

2009-12-31T09:23:00.002+07:00

In the last period of my study, I choose to revive once again this blog
Well, actually I need this blog as journal on research for completing my study
And I think, I can get some help regarding my work through this media

Software that I use for this research is kinda rare
Not much biochemical researcher publish their experience on DOVIS 2.0
I hope anybody after me that using DOVIS 2.0 can get some information from the blog

regards,

Muhammad H Hilman