Tips in Mex Fortran, linux version

Starting from the day before yesterday, I need to write a Matlab interface for a Fortran source code, which is almost a black box for me, so that I can use "mex" to compile it and call it in Matlab.

The first thing is the compiler. In Windows, you can only choose a specific compiler, say, C/C++ or Fortran. So if you work with both C and Fortran code, you will have to use "mex -setup" from time to time, which is kinda annoying for a lazy person like me. But in Linux, you can work on a configuration file so that Matlab will automatically select the compiler for you.

First, in "/opt/R2009a/unix/bin/mexopts.sh", you can see the following segment:

#
FC='g95'
FFLAGS='-fexceptions'
FFLAGS="$FFLAGS -fPIC -fno-omit-frame-pointer"
FLIBS="$RPATH $MLIBS -lm"
FOPTIMFLAGS='-O'
FDEBUGFLAGS='-g'
#

The first line indicates the compiler for Fortran. "g95" is not provided, so, we will change it to gfortran which I think comes with Ubuntu. Thus, change this segement into:

#
FC='gfortran'
FFLAGS='-fexceptions'
FFLAGS="$FFLAGS -fPIC -fno-omit-frame-pointer"
FLIBS="$RPATH $MLIBS -lm"
FOPTIMFLAGS='-O'
FDEBUGFLAGS='-g'
#

Then, in Matlab, if you type
mex -setup

You will see something like:
The options files available for mex are:

1: /opt/R2009a/unix/bin/gccopts.sh :
Template Options file for building gcc MEX-files

2: /opt/R2009a/unix/bin/mexopts.sh :
Template Options file for building MEX-files via the system ANSI compiler

Choose 2. Then it's ok to compile.

The next thing is the interface. The help in Matlab has everything you know to create a wrapper, even some examples for you to follow. So although I know nothing about Fortran, I managed to write a "almost" complete interface which passed the compilation.

However, there're several important tips that costs me a whole day to figure out.

1. The name of the source file must be ".F", otherwise it won't compile.
2. If the source code you want to wrap was not developed by you, be very careful about all the data types in that code. For example, if one input for that function is "REAL", then it is 4-byte floating number. And in Matlab, unless specified, everything will be "double", which is 8-byte floating number. If you pass the double value directly into it, the value will NOT be preserved. So when you call the function in Matlab, use something like "nlam = int32(nlam);
   
   beta = single(beta);" Also, inside the interface, use something like "mxCopyPtrToReal4(beta_pr,beta,size)".
3. The next thing is managing the output. When you create the output matrices, do not use mxCreateDoubleMatrix. Use "mxCreateNumericMatrix", which will let you to specify the output types like int32 or single.
   

How-To: What should you do if you deleted files in NTFS by mistake

OK. Here is how it happens. One day, I was using the filezilla, pulling down a tiny little file to my hard disk of the desktop machine in my office. It is the major machine I use for research, and all my LaTeX papers, matlab codes are there.

Then, I select the whole "Research" disk, and downloaded that file into it. Then, assuming I am still selecting the tiny file on the remote server, I hit "delete" button. The computer seems to be hanging there with no response, which happens quite a lot when I use filezilla, by the way. So I force quit (thank god).

Then, after maybe a few minutes, I found that all my codes are gone somehow. WTF?!

It was all my fault, can't blame anyone.

So what I did was I delete almost everything in a NTFS disk, when I was using Ubuntu Linux. Bad news. There is no trash can, and everything is somehow "gone forever".

OK, enough for my miserable story.

The first thing I try is under Windows, a commercial software called "Recover my files". It will recover a lot of files, only without the file names. But file names and original locations are SO important because there are thousands of them and most of them are codes, which basically called by its name.

Then, I tried free wares in Ubuntu, such as ntfsundelete and photorec. They all can recover the files, but not the name and location. Well, at least I can recover them, it just takes time. My final choice is photorec.

There is one oerticular software that can recover your file, name and location, though. It is called: "Autopsy". Also a linux free ware, but it works like a webpage, and you can only recover the file one by one. But I did use it to recover a lot of vital source code.

One tip is, after you hurt your disk, you can use "ddrescue" to mirror the whole disk to another externel hard disk (should be much bigger than the one you want to backup). Then, the file you create works just like a disk, and yu can recover based on that without further damage.

The only thing you can do to prevent this from happening is to back up your system regularly. The reason that I can survive this with only one week of frustraion is that I uploaded the most vital part of my work to a remote server, for computation purpose. Because of that, I only need to recover a very small ratio, using the combanation of those softwares.

But starting from now, I will start to use file sync softwares to back up my works to another disk on a regular basis. My recommendation is Grsync. You can setup some commonly profiles, and just click excecute it will sync by only dealing with the differences. Very fast.

You can also write a script to automaticly sync the folders, say, every night. I do not have the time right now. Here are some useful links:

https://help.ubuntu.com/community/BackupYourSystem#grsync
http://www.unixgeeks.org/security/newbie/unix/cron-1.html
http://linuxbasement.com/content/backups-using-rsync-bash-cron
http://linuxgazette.net/104/odonovan.html