I try to run a C implementation of Sift feature descriptor executable from matlab at linux. The script I run and the executable at the some folder and executable is run by the following
./sift <tmp.pgm >tmp.key
and I trued to run it on Matlab with followings but none of them worked
eval('!./sift <tmp.pgm >tmp.key');
system('./sift <tmp.pgm >tmp.key');
unix('./sift <tmp.pgm >tmp.key');
I also check the executable from terminal and it works without any flaw. Is there any other way to do that or Do i have any slight mistake?
Your syntax looks right.
The -1 status means it's probably failing to find or launch sift at all. I know this is basic (and I think someone else mentioned it), but is your Matlab program running from the same directory that sift is in when it calls it? The system() function evaluates paths with respect to the Matlab session's current directory, not the location of the calling script. If your script has called cd for other reasons, that'll affect it. Check your current directory with pwd and do an ls and exist('./sift', 'file') to make sure it's there.
If this is the case, you could make it more robust by calling sift with an absolute path, maybe calculated at run time using fileparts(mfilename('fullpath')) in the script.
I figure out the problem as the path /matlab/bin/glnxa64/matlab_helper has permission problem. After I check the problem, everything started to work correctly.
I had the same problem of permission. Just adding solution for others to see as i had hard time finding the solution.
Open terminal and type
cd \path_of_your_file
sudo chmod -R 777
it will ask for your password and will permit to run the exe. Hugs..
Related
When running scripts in bash, I have to write ./ in the beginning:
$ ./manage.py syncdb
If I don't, I get an error message:
$ manage.py syncdb
-bash: manage.py: command not found
What is the reason for this? I thought . is an alias for current folder, and therefore these two calls should be equivalent.
I also don't understand why I don't need ./ when running applications, such as:
user:/home/user$ cd /usr/bin
user:/usr/bin$ git
(which runs without ./)
Because on Unix, usually, the current directory is not in $PATH.
When you type a command the shell looks up a list of directories, as specified by the PATH variable. The current directory is not in that list.
The reason for not having the current directory on that list is security.
Let's say you're root and go into another user's directory and type sl instead of ls. If the current directory is in PATH, the shell will try to execute the sl program in that directory (since there is no other sl program). That sl program might be malicious.
It works with ./ because POSIX specifies that a command name that contain a / will be used as a filename directly, suppressing a search in $PATH. You could have used full path for the exact same effect, but ./ is shorter and easier to write.
EDIT
That sl part was just an example. The directories in PATH are searched sequentially and when a match is made that program is executed. So, depending on how PATH looks, typing a normal command may or may not be enough to run the program in the current directory.
When bash interprets the command line, it looks for commands in locations described in the environment variable $PATH. To see it type:
echo $PATH
You will have some paths separated by colons. As you will see the current path . is usually not in $PATH. So Bash cannot find your command if it is in the current directory. You can change it by having:
PATH=$PATH:.
This line adds the current directory in $PATH so you can do:
manage.py syncdb
It is not recommended as it has security issue, plus you can have weird behaviours, as . varies upon the directory you are in :)
Avoid:
PATH=.:$PATH
As you can “mask” some standard command and open the door to security breach :)
Just my two cents.
Your script, when in your home directory will not be found when the shell looks at the $PATH environment variable to find your script.
The ./ says 'look in the current directory for my script rather than looking at all the directories specified in $PATH'.
When you include the '.' you are essentially giving the "full path" to the executable bash script, so your shell does not need to check your PATH variable. Without the '.' your shell will look in your PATH variable (which you can see by running echo $PATH to see if the command you typed lives in any of the folders on your PATH. If it doesn't (as is the case with manage.py) it says it can't find the file. It is considered bad practice to include the current directory on your PATH, which is explained reasonably well here: http://www.faqs.org/faqs/unix-faq/faq/part2/section-13.html
On *nix, unlike Windows, the current directory is usually not in your $PATH variable. So the current directory is not searched when executing commands. You don't need ./ for running applications because these applications are in your $PATH; most likely they are in /bin or /usr/bin.
This question already has some awesome answers, but I wanted to add that, if your executable is on the PATH, and you get very different outputs when you run
./executable
to the ones you get if you run
executable
(let's say you run into error messages with the one and not the other), then the problem could be that you have two different versions of the executable on your machine: one on the path, and the other not.
Check this by running
which executable
and
whereis executable
It fixed my issues...I had three versions of the executable, only one of which was compiled correctly for the environment.
Rationale for the / POSIX PATH rule
The rule was mentioned at: Why do you need ./ (dot-slash) before executable or script name to run it in bash? but I would like to explain why I think that is a good design in more detail.
First, an explicit full version of the rule is:
if the path contains / (e.g. ./someprog, /bin/someprog, ./bin/someprog): CWD is used and PATH isn't
if the path does not contain / (e.g. someprog): PATH is used and CWD isn't
Now, suppose that running:
someprog
would search:
relative to CWD first
relative to PATH after
Then, if you wanted to run /bin/someprog from your distro, and you did:
someprog
it would sometimes work, but others it would fail, because you might be in a directory that contains another unrelated someprog program.
Therefore, you would soon learn that this is not reliable, and you would end up always using absolute paths when you want to use PATH, therefore defeating the purpose of PATH.
This is also why having relative paths in your PATH is a really bad idea. I'm looking at you, node_modules/bin.
Conversely, suppose that running:
./someprog
Would search:
relative to PATH first
relative to CWD after
Then, if you just downloaded a script someprog from a git repository and wanted to run it from CWD, you would never be sure that this is the actual program that would run, because maybe your distro has a:
/bin/someprog
which is in you PATH from some package you installed after drinking too much after Christmas last year.
Therefore, once again, you would be forced to always run local scripts relative to CWD with full paths to know what you are running:
"$(pwd)/someprog"
which would be extremely annoying as well.
Another rule that you might be tempted to come up with would be:
relative paths use only PATH, absolute paths only CWD
but once again this forces users to always use absolute paths for non-PATH scripts with "$(pwd)/someprog".
The / path search rule offers a simple to remember solution to the about problem:
slash: don't use PATH
no slash: only use PATH
which makes it super easy to always know what you are running, by relying on the fact that files in the current directory can be expressed either as ./somefile or somefile, and so it gives special meaning to one of them.
Sometimes, is slightly annoying that you cannot search for some/prog relative to PATH, but I don't see a saner solution to this.
When the script is not in the Path its required to do so. For more info read http://www.tldp.org/LDP/Bash-Beginners-Guide/html/sect_02_01.html
All has great answer on the question, and yes this is only applicable when running it on the current directory not unless you include the absolute path. See my samples below.
Also, the (dot-slash) made sense to me when I've the command on the child folder tmp2 (/tmp/tmp2) and it uses (double dot-slash).
SAMPLE:
[fifiip-172-31-17-12 tmp]$ ./StackO.sh
Hello Stack Overflow
[fifi#ip-172-31-17-12 tmp]$ /tmp/StackO.sh
Hello Stack Overflow
[fifi#ip-172-31-17-12 tmp]$ mkdir tmp2
[fifi#ip-172-31-17-12 tmp]$ cd tmp2/
[fifi#ip-172-31-17-12 tmp2]$ ../StackO.sh
Hello Stack Overflow
I am new here.
Could anyone help me, on how to use yarpgen to generate a random c program.
I tried running the run_gen.py script that I saw in the yarpgen readme.
But, I got a warning and an error like this:
Warning: please set YARPGEN_HOME envirnoment variable to point to test generator path, using C:\Users\..\Python\Python36-32\yarpgen-master for now
and
File C:\Users\..\Python\Python36-32\yarpgen-master\yarpgen wasn't found
Any help would be much appreciated.
Thanks in advance !
The warning very likely points to the source of the problem, run_gen does not know where the other parts of yarpgen are installed.
First, note down the directory you installed/copied yarpgen to.
Then open a command shell. Type this:
cd <where run_gen.py is>
set YARPGEN_HOME=<the path you just noted down>
run_gen.py
If this works, you can write a batch script, that contains the set YARPGEN_HOME=... line and then calls run_gen.py. If the directory where run_gen.py is located is not on your PATH environment variable, call run_gen.py with the full absolute path in the batch script:
set YARPGEN_HOME=<the path to yarpgen>
python3 <absolute_path_to>\run_gen.py
Then you can call your batch script.
You may have to adjust the python3 command depending on the executable Python 3 installed on your machine (it may be just python on Windows).
When I tried this after building with cygwin, I noticed that I had to rename yarpgen.exe to yarpgen to make it work.
When running scripts in bash, I have to write ./ in the beginning:
$ ./manage.py syncdb
If I don't, I get an error message:
$ manage.py syncdb
-bash: manage.py: command not found
What is the reason for this? I thought . is an alias for current folder, and therefore these two calls should be equivalent.
I also don't understand why I don't need ./ when running applications, such as:
user:/home/user$ cd /usr/bin
user:/usr/bin$ git
(which runs without ./)
Because on Unix, usually, the current directory is not in $PATH.
When you type a command the shell looks up a list of directories, as specified by the PATH variable. The current directory is not in that list.
The reason for not having the current directory on that list is security.
Let's say you're root and go into another user's directory and type sl instead of ls. If the current directory is in PATH, the shell will try to execute the sl program in that directory (since there is no other sl program). That sl program might be malicious.
It works with ./ because POSIX specifies that a command name that contain a / will be used as a filename directly, suppressing a search in $PATH. You could have used full path for the exact same effect, but ./ is shorter and easier to write.
EDIT
That sl part was just an example. The directories in PATH are searched sequentially and when a match is made that program is executed. So, depending on how PATH looks, typing a normal command may or may not be enough to run the program in the current directory.
When bash interprets the command line, it looks for commands in locations described in the environment variable $PATH. To see it type:
echo $PATH
You will have some paths separated by colons. As you will see the current path . is usually not in $PATH. So Bash cannot find your command if it is in the current directory. You can change it by having:
PATH=$PATH:.
This line adds the current directory in $PATH so you can do:
manage.py syncdb
It is not recommended as it has security issue, plus you can have weird behaviours, as . varies upon the directory you are in :)
Avoid:
PATH=.:$PATH
As you can “mask” some standard command and open the door to security breach :)
Just my two cents.
Your script, when in your home directory will not be found when the shell looks at the $PATH environment variable to find your script.
The ./ says 'look in the current directory for my script rather than looking at all the directories specified in $PATH'.
When you include the '.' you are essentially giving the "full path" to the executable bash script, so your shell does not need to check your PATH variable. Without the '.' your shell will look in your PATH variable (which you can see by running echo $PATH to see if the command you typed lives in any of the folders on your PATH. If it doesn't (as is the case with manage.py) it says it can't find the file. It is considered bad practice to include the current directory on your PATH, which is explained reasonably well here: http://www.faqs.org/faqs/unix-faq/faq/part2/section-13.html
On *nix, unlike Windows, the current directory is usually not in your $PATH variable. So the current directory is not searched when executing commands. You don't need ./ for running applications because these applications are in your $PATH; most likely they are in /bin or /usr/bin.
This question already has some awesome answers, but I wanted to add that, if your executable is on the PATH, and you get very different outputs when you run
./executable
to the ones you get if you run
executable
(let's say you run into error messages with the one and not the other), then the problem could be that you have two different versions of the executable on your machine: one on the path, and the other not.
Check this by running
which executable
and
whereis executable
It fixed my issues...I had three versions of the executable, only one of which was compiled correctly for the environment.
Rationale for the / POSIX PATH rule
The rule was mentioned at: Why do you need ./ (dot-slash) before executable or script name to run it in bash? but I would like to explain why I think that is a good design in more detail.
First, an explicit full version of the rule is:
if the path contains / (e.g. ./someprog, /bin/someprog, ./bin/someprog): CWD is used and PATH isn't
if the path does not contain / (e.g. someprog): PATH is used and CWD isn't
Now, suppose that running:
someprog
would search:
relative to CWD first
relative to PATH after
Then, if you wanted to run /bin/someprog from your distro, and you did:
someprog
it would sometimes work, but others it would fail, because you might be in a directory that contains another unrelated someprog program.
Therefore, you would soon learn that this is not reliable, and you would end up always using absolute paths when you want to use PATH, therefore defeating the purpose of PATH.
This is also why having relative paths in your PATH is a really bad idea. I'm looking at you, node_modules/bin.
Conversely, suppose that running:
./someprog
Would search:
relative to PATH first
relative to CWD after
Then, if you just downloaded a script someprog from a git repository and wanted to run it from CWD, you would never be sure that this is the actual program that would run, because maybe your distro has a:
/bin/someprog
which is in you PATH from some package you installed after drinking too much after Christmas last year.
Therefore, once again, you would be forced to always run local scripts relative to CWD with full paths to know what you are running:
"$(pwd)/someprog"
which would be extremely annoying as well.
Another rule that you might be tempted to come up with would be:
relative paths use only PATH, absolute paths only CWD
but once again this forces users to always use absolute paths for non-PATH scripts with "$(pwd)/someprog".
The / path search rule offers a simple to remember solution to the about problem:
slash: don't use PATH
no slash: only use PATH
which makes it super easy to always know what you are running, by relying on the fact that files in the current directory can be expressed either as ./somefile or somefile, and so it gives special meaning to one of them.
Sometimes, is slightly annoying that you cannot search for some/prog relative to PATH, but I don't see a saner solution to this.
When the script is not in the Path its required to do so. For more info read http://www.tldp.org/LDP/Bash-Beginners-Guide/html/sect_02_01.html
All has great answer on the question, and yes this is only applicable when running it on the current directory not unless you include the absolute path. See my samples below.
Also, the (dot-slash) made sense to me when I've the command on the child folder tmp2 (/tmp/tmp2) and it uses (double dot-slash).
SAMPLE:
[fifiip-172-31-17-12 tmp]$ ./StackO.sh
Hello Stack Overflow
[fifi#ip-172-31-17-12 tmp]$ /tmp/StackO.sh
Hello Stack Overflow
[fifi#ip-172-31-17-12 tmp]$ mkdir tmp2
[fifi#ip-172-31-17-12 tmp]$ cd tmp2/
[fifi#ip-172-31-17-12 tmp2]$ ../StackO.sh
Hello Stack Overflow
When running scripts in bash, I have to write ./ in the beginning:
$ ./manage.py syncdb
If I don't, I get an error message:
$ manage.py syncdb
-bash: manage.py: command not found
What is the reason for this? I thought . is an alias for current folder, and therefore these two calls should be equivalent.
I also don't understand why I don't need ./ when running applications, such as:
user:/home/user$ cd /usr/bin
user:/usr/bin$ git
(which runs without ./)
Because on Unix, usually, the current directory is not in $PATH.
When you type a command the shell looks up a list of directories, as specified by the PATH variable. The current directory is not in that list.
The reason for not having the current directory on that list is security.
Let's say you're root and go into another user's directory and type sl instead of ls. If the current directory is in PATH, the shell will try to execute the sl program in that directory (since there is no other sl program). That sl program might be malicious.
It works with ./ because POSIX specifies that a command name that contain a / will be used as a filename directly, suppressing a search in $PATH. You could have used full path for the exact same effect, but ./ is shorter and easier to write.
EDIT
That sl part was just an example. The directories in PATH are searched sequentially and when a match is made that program is executed. So, depending on how PATH looks, typing a normal command may or may not be enough to run the program in the current directory.
When bash interprets the command line, it looks for commands in locations described in the environment variable $PATH. To see it type:
echo $PATH
You will have some paths separated by colons. As you will see the current path . is usually not in $PATH. So Bash cannot find your command if it is in the current directory. You can change it by having:
PATH=$PATH:.
This line adds the current directory in $PATH so you can do:
manage.py syncdb
It is not recommended as it has security issue, plus you can have weird behaviours, as . varies upon the directory you are in :)
Avoid:
PATH=.:$PATH
As you can “mask” some standard command and open the door to security breach :)
Just my two cents.
Your script, when in your home directory will not be found when the shell looks at the $PATH environment variable to find your script.
The ./ says 'look in the current directory for my script rather than looking at all the directories specified in $PATH'.
When you include the '.' you are essentially giving the "full path" to the executable bash script, so your shell does not need to check your PATH variable. Without the '.' your shell will look in your PATH variable (which you can see by running echo $PATH to see if the command you typed lives in any of the folders on your PATH. If it doesn't (as is the case with manage.py) it says it can't find the file. It is considered bad practice to include the current directory on your PATH, which is explained reasonably well here: http://www.faqs.org/faqs/unix-faq/faq/part2/section-13.html
On *nix, unlike Windows, the current directory is usually not in your $PATH variable. So the current directory is not searched when executing commands. You don't need ./ for running applications because these applications are in your $PATH; most likely they are in /bin or /usr/bin.
This question already has some awesome answers, but I wanted to add that, if your executable is on the PATH, and you get very different outputs when you run
./executable
to the ones you get if you run
executable
(let's say you run into error messages with the one and not the other), then the problem could be that you have two different versions of the executable on your machine: one on the path, and the other not.
Check this by running
which executable
and
whereis executable
It fixed my issues...I had three versions of the executable, only one of which was compiled correctly for the environment.
Rationale for the / POSIX PATH rule
The rule was mentioned at: Why do you need ./ (dot-slash) before executable or script name to run it in bash? but I would like to explain why I think that is a good design in more detail.
First, an explicit full version of the rule is:
if the path contains / (e.g. ./someprog, /bin/someprog, ./bin/someprog): CWD is used and PATH isn't
if the path does not contain / (e.g. someprog): PATH is used and CWD isn't
Now, suppose that running:
someprog
would search:
relative to CWD first
relative to PATH after
Then, if you wanted to run /bin/someprog from your distro, and you did:
someprog
it would sometimes work, but others it would fail, because you might be in a directory that contains another unrelated someprog program.
Therefore, you would soon learn that this is not reliable, and you would end up always using absolute paths when you want to use PATH, therefore defeating the purpose of PATH.
This is also why having relative paths in your PATH is a really bad idea. I'm looking at you, node_modules/bin.
Conversely, suppose that running:
./someprog
Would search:
relative to PATH first
relative to CWD after
Then, if you just downloaded a script someprog from a git repository and wanted to run it from CWD, you would never be sure that this is the actual program that would run, because maybe your distro has a:
/bin/someprog
which is in you PATH from some package you installed after drinking too much after Christmas last year.
Therefore, once again, you would be forced to always run local scripts relative to CWD with full paths to know what you are running:
"$(pwd)/someprog"
which would be extremely annoying as well.
Another rule that you might be tempted to come up with would be:
relative paths use only PATH, absolute paths only CWD
but once again this forces users to always use absolute paths for non-PATH scripts with "$(pwd)/someprog".
The / path search rule offers a simple to remember solution to the about problem:
slash: don't use PATH
no slash: only use PATH
which makes it super easy to always know what you are running, by relying on the fact that files in the current directory can be expressed either as ./somefile or somefile, and so it gives special meaning to one of them.
Sometimes, is slightly annoying that you cannot search for some/prog relative to PATH, but I don't see a saner solution to this.
When the script is not in the Path its required to do so. For more info read http://www.tldp.org/LDP/Bash-Beginners-Guide/html/sect_02_01.html
All has great answer on the question, and yes this is only applicable when running it on the current directory not unless you include the absolute path. See my samples below.
Also, the (dot-slash) made sense to me when I've the command on the child folder tmp2 (/tmp/tmp2) and it uses (double dot-slash).
SAMPLE:
[fifiip-172-31-17-12 tmp]$ ./StackO.sh
Hello Stack Overflow
[fifi#ip-172-31-17-12 tmp]$ /tmp/StackO.sh
Hello Stack Overflow
[fifi#ip-172-31-17-12 tmp]$ mkdir tmp2
[fifi#ip-172-31-17-12 tmp]$ cd tmp2/
[fifi#ip-172-31-17-12 tmp2]$ ../StackO.sh
Hello Stack Overflow
I'm running Matlab 7.8.0 under Windows.
I am calling an external utility using dos() which creates a file in the current directory.
I the file is created correctly, but it cannot be seen by exist or fopen, which return 0 and -1 respectively. The filename is correct!
>> pwd
ans =
I:\
>> ls
file1.asc file2.asc file3.asc
>> exist('file1.asc') % this file was there before
ans =
2
>> exist('file2.asc') % this file is newly created
ans =
0
to confirm it's not an odd/problematic filename, I checked from a Cygwin shell:
/cygdrive/i/ $ if [ -f file2.asc ]; then echo "OK"; fi
OK
So the file is good. I tried renaming it
/cygdrive/i/ $ mv file2.asc test
and in Matlab
>> ls
file1.asc file3.asc test
>> exist('test')
ans =
0
If I exit and restart Matlab it works fine. But I need to dynamically create the file and then access it!
Very mysterious.
You could try:
The rehash command to see if that helps.
The two-argument version of exists: exist('foo.txt', 'file')
The Matlab exist() command is not a simple filesystem operation; it also looks at variables, functions, etc. Since you're on I:, I'm assuming that's a network drive, and you're probably running in to the dir contents caching problem that Jonas mentions.
Here are a couple other workarounds, in case nsanders' two-arg exist() or Jonas' change notification fixes don't work for you.
Try using absolute paths to the files, like "fopen('I:\file2.asc')", instead of relative paths and pwd. Matlab will treat unqualified filenames as "partial paths" for both exist() and fopen(), and that interacts with the directory info caching. Ls() does not work with partial paths, which may be why it can see the file and the other functions can't.
You can use Java from within Matlab to do a simpler file existence test.
java.io.File('file2.asc').exists()
Or since the ls() command is showing the file you want, you can just implement the file existence check on top of ls.
ismember({'file2.asc'}, ls())
The "{ }" is necessary to make ismember() operate at the string level instead of the char level.
If you're still having trouble reading it, try doing a lower level read with Java from within Matlab. That will tell you whether it's specifically Matlab's I/O functions that are having trouble, or of the process itself lacks access to the file. Try this. If you get a char out of it, that means your Matlab.exe process can see the file.
istr = java.io.FileInputStream('file2.asc')
c = char(istr.read())
On Windows, I used to get change handle notification warnings at startup until I turned the warnings off. I don't have 7.8 at hand right now, but the warning may be off by default.
As explained on the MathWorks site, if Windows runs out of change notification handles, it will not be able to properly "sense" whether the content of a directory has changed, which might be causing your problems.
Are you sure that MATLAB is running as the same user as explorer is? If MATLAB requires elevated permissions to run then the drive mappings may be different and you could find that the I:\ drive is not mapped.
To fix this you would need to somehow map the I: drive under elevated permissions.