Re: [galaxy-user] server error trying to DL data from galaxy on cloud
Hello, I'm trying to download the library files I processed on my galaxy cloud instance, but I'm getting an error. At the top (on the right panel) it says "Server Error" and then lists the URL where the data should be and then lists: Module paste.exceptions.errormiddleware:143 in __call__ << try: __traceback_supplement__ = Supplement, self, environ app_iter = self.application(environ, start_response) return self.make_catching_iter(app_iter, environ) except:>> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ << try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred>> environ, self.app) Module paste.wsgilib:544 in intercept_output << try: for item in app_iter: output.write(item) finally: if hasattr(app_iter, 'close'):>> output.write(item) MemoryError: out of memory Is there some easy fix to this? I'd really like to get that data off of the cloud instance and be able to terminate it. thanks, karl
Hi Karl, As you see from the error message, you seem to be getting this error because the machine is running out of memory. This can in part be caused by a configuration option that might be set in Galaxy's universe_wsgi.ini file (see below). Did you have any jobs running while trying to download the file? Waiting until those finish might free up some memory. A thing to try is to connect to the instance, edit Galaxy's universe_wsgi.ini file to se debug = False, restart Galaxy and try again. Are you familiar with that at all? The basic steps are as follows: [local]$ ssh -i <path to your AWS private key file> ubuntu@<instance public IP> [ec2]$ sudo su galaxy [ec2]$ cd /mnt/galaxyTools/galaxy-central [ec2]$ vi universe_wsgi.ini -- edit file (around line 226) to set: debug = False [ec2]$ sh run.sh --stop-daemon [ec2]$ sh run.sh --daemon Yet another option is to connect the instance in the same way, look through the data library on the file system and manually copy the file out of the instance. You can use the following command to copy the file to your local instance: [local]$ scp -i <path to your AWS private key file> ubuntu@<instance public IP>:/mnt/galaxyData/files/000/dataset_<ID>.dat . Let us know if none of this works, Enis On Mon, Mar 28, 2011 at 12:02 PM, <karlerhard@berkeley.edu> wrote:
Hello,
I'm trying to download the library files I processed on my galaxy cloud instance, but I'm getting an error. At the top (on the right panel) it says "Server Error" and then lists the URL where the data should be and then lists:
Module paste.exceptions.errormiddleware:143 in __call__ << try: __traceback_supplement__ = Supplement, self, environ app_iter = self.application(environ, start_response) return self.make_catching_iter(app_iter, environ) except:>> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ << try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred>> environ, self.app) Module paste.wsgilib:544 in intercept_output << try: for item in app_iter: output.write(item) finally: if hasattr(app_iter, 'close'):>> output.write(item) MemoryError: out of memory
Is there some easy fix to this? I'd really like to get that data off of the cloud instance and be able to terminate it.
thanks,
karl
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hello Enis, Thanks for the quick response and suggestions. I actually did have a job running while I tried to download a file the first time, that's the first time it gave the error message. But the jobs have long since finished and it's still giving the error message. I've been able to edit the universe_wsgi.ini file to "debug = False", but now I'm getting an "Internal server error" when I try to reload the galaxy instance. Should I be signed out at the command-line to reload galaxy from a browser? Forgive my simplicity, I'm really not at all command-line savvy. Also, another extremely basic problem I have is I just don't know where the data library that holds my files is located. Any help would be greatly appreciated. best, karl
Hi Karl, As you see from the error message, you seem to be getting this error because the machine is running out of memory. This can in part be caused by a configuration option that might be set in Galaxy's universe_wsgi.ini file (see below). Did you have any jobs running while trying to download the file? Waiting until those finish might free up some memory.
A thing to try is to connect to the instance, edit Galaxy's universe_wsgi.ini file to se debug = False, restart Galaxy and try again. Are you familiar with that at all? The basic steps are as follows: [local]$ ssh -i <path to your AWS private key file> ubuntu@<instance public IP> [ec2]$ sudo su galaxy [ec2]$ cd /mnt/galaxyTools/galaxy-central [ec2]$ vi universe_wsgi.ini -- edit file (around line 226) to set: debug = False [ec2]$ sh run.sh --stop-daemon [ec2]$ sh run.sh --daemon
Yet another option is to connect the instance in the same way, look through the data library on the file system and manually copy the file out of the instance. You can use the following command to copy the file to your local instance: [local]$ scp -i <path to your AWS private key file> ubuntu@<instance public IP>:/mnt/galaxyData/files/000/dataset_<ID>.dat .
Let us know if none of this works, Enis
On Mon, Mar 28, 2011 at 12:02 PM, <karlerhard@berkeley.edu> wrote:
Hello,
I'm trying to download the library files I processed on my galaxy cloud instance, but I'm getting an error. At the top (on the right panel) it says "Server Error" and then lists the URL where the data should be and then lists:
Module paste.exceptions.errormiddleware:143 in __call__ << try: __traceback_supplement__ = Supplement, self, environ app_iter = self.application(environ, start_response) return self.make_catching_iter(app_iter, environ) except:>> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ << try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred>> environ, self.app) Module paste.wsgilib:544 in intercept_output << try: for item in app_iter: output.write(item) finally: if hasattr(app_iter, 'close'):>> output.write(item) MemoryError: out of memory
Is there some easy fix to this? I'd really like to get that data off of the cloud instance and be able to terminate it.
thanks,
karl
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Karl, Hmm, not having Galaxy accessible is definitely not a step in the right direction. Being signed into command line is not an issue; something else must have gone wrong. To start, please take a look at the (bottom of) galaxy log file (and email the relevant part if you don't see how to fix it immediately); the file is saved as /mnt/galaxyTools/galaxy-central/paster.log As far as the location of the files in data libraries, they should be stored in the same location as history datasets, namely /mnt/galaxyData/files/000/dataset_<ID>.dat Because all of the datasets are named simply based on the database ID, it won't necessarily be obvious which file to get without doing some (python) coding or doing some guess work. If you know how large your files is, you can easily narrow your choices down by listing the contents of the given directory and sorting it by size (using command ls -lS), then pulling out the file(s) that you want. If several files are of approx. the same size, open them up and see which one you want. Good luck and let us know if you have any more trouble, Enis On Mon, Mar 28, 2011 at 3:35 PM, <karlerhard@berkeley.edu> wrote:
Hello Enis,
Thanks for the quick response and suggestions. I actually did have a job running while I tried to download a file the first time, that's the first time it gave the error message. But the jobs have long since finished and it's still giving the error message.
I've been able to edit the universe_wsgi.ini file to "debug = False", but now I'm getting an "Internal server error" when I try to reload the galaxy instance. Should I be signed out at the command-line to reload galaxy from a browser? Forgive my simplicity, I'm really not at all command-line savvy.
Also, another extremely basic problem I have is I just don't know where the data library that holds my files is located. Any help would be greatly appreciated.
best,
karl
Hi Karl, As you see from the error message, you seem to be getting this error because the machine is running out of memory. This can in part be caused by a configuration option that might be set in Galaxy's universe_wsgi.ini file (see below). Did you have any jobs running while trying to download the file? Waiting until those finish might free up some memory.
A thing to try is to connect to the instance, edit Galaxy's universe_wsgi.ini file to se debug = False, restart Galaxy and try again. Are you familiar with that at all? The basic steps are as follows: [local]$ ssh -i <path to your AWS private key file> ubuntu@<instance public IP> [ec2]$ sudo su galaxy [ec2]$ cd /mnt/galaxyTools/galaxy-central [ec2]$ vi universe_wsgi.ini -- edit file (around line 226) to set: debug = False [ec2]$ sh run.sh --stop-daemon [ec2]$ sh run.sh --daemon
Yet another option is to connect the instance in the same way, look through the data library on the file system and manually copy the file out of the instance. You can use the following command to copy the file to your local instance: [local]$ scp -i <path to your AWS private key file> ubuntu@<instance public IP>:/mnt/galaxyData/files/000/dataset_<ID>.dat .
Let us know if none of this works, Enis
On Mon, Mar 28, 2011 at 12:02 PM, <karlerhard@berkeley.edu> wrote:
Hello,
I'm trying to download the library files I processed on my galaxy cloud instance, but I'm getting an error. At the top (on the right panel) it says "Server Error" and then lists the URL where the data should be and then lists:
Module paste.exceptions.errormiddleware:143 in __call__ << try: __traceback_supplement__ = Supplement, self, environ app_iter = self.application(environ, start_response) return self.make_catching_iter(app_iter, environ) except:>> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ << try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred>> environ, self.app) Module paste.wsgilib:544 in intercept_output << try: for item in app_iter: output.write(item) finally: if hasattr(app_iter, 'close'):>> output.write(item) MemoryError: out of memory
Is there some easy fix to this? I'd really like to get that data off of the cloud instance and be able to terminate it.
thanks,
karl
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
-
Enis Afgan -
karlerhard＠berkeley.edu