Hi, Anyone here testing, experimenting with R and nginx ? Im trying to setup nginx to serve R scripts via CGI using Rserve, FastRWeb modules as described here: http://jayemerson.blogspot.fi/2011/10/setting-up-f... My nginx is configured like: location ~ ^/cgi-bin/.*\.cgi$ { gzip off; fastcgi_pass unix:/opt/sdr/report/ws/fastcgi_temp/nginx-fcgi.sock; fastcgi_read_timeout 5m; fastcgi_index index.cgi; #fastcgi_buffers 8 4k; # # You may copy and paste the lines under or use include directive # include /etc/nginx/nginx-fcgi.conf; # In this example all is in one file # fastcgi_param SCRIPT_NAME $fastcgi_script_name; fastcgi_param QUERY_STRING $query_string; fastcgi_param REQUEST_METHOD $request_method; fastcgi_param CONTENT_TYPE $content_type; fastcgi_param CONTENT_LENGTH $content_length; fastcgi_param GATEWAY_INTERFACE CGI/1.1; fastcgi_param SERVER_SOFTWARE nginx; fastcgi_param SCRIPT_NAME $fastcgi_script_name; fastcgi_param REQUEST_URI $request_uri; fastcgi_param DOCUMENT_URI $document_uri; fastcgi_param DOCUMENT_ROOT /opt/sdr/report/docroot; fastcgi_param SERVER_PROTOCOL $server_protocol; fastcgi_param REMOTE_ADDR $remote_addr; fastcgi_param REMOTE_PORT $remote_port; fastcgi_param SERVER_ADDR $server_addr; fastcgi_param SERVER_PORT $server_port; fastcgi_param SERVER_NAME $server_name; } and Im using fcgiwrap from http://nginx.localdomain.pl/wiki/FcgiWrap. CGI scripts work fine but Im not able to any R scripts probable due R being not correctly called via nginx.conf ... I am trying something like: http://localhost/cgi-bin/R/foo.png?n=500 and R is a binary file under cgi-bin directory which should call FastRWeb ... Any pointers, help ? thanks, Stefan
on 2013-02-19 13:49
on 2013-02-19 14:50
Does the R cgi script filename end in .cgi ? That's what you specify, it appears. On Tue, Feb 19, 2013 at 7:47 AM, Stefan Parvu <sparvu@systemdatarecorder.org
on 2013-02-19 15:51
On 08:50 Tue 19 Feb , Harold Sinclair wrote: > Does the R cgi script filename end in .cgi ? That's what you specify, it > appears. No, it does not end with cgi since the R scripts will not be called directly by nginx. As I understood I should call the R scripts like: http://localhost/cgi-bin/R/foo where there is a R binary file under cgi-bin which will proxy those to FastRWeb and Rserve R modules. So under cgi-bin there are no R scripts whatsoever, but they usually will go under: /opt/sdr/report/var/FastRWeb/web.R directory. Now my problem seems to be related how the R binary under cgi-bin will ever be called via CGI and further FastRWeb ... since my nginx.conf knows nada about R being called. Currently my nginx.conf is configured to run anything ending .cgi as cgi scripts ... /opt/sdr/report/docroot/cgi-bin $ ls -lrt total 60 -rwxr-x--- 1 sdr sdr 3715 Feb 19 12:00 initial.cgi -rwxr-xr-x 1 sdr sdr 55932 Feb 19 13:53 R $ file R R: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.24, BuildID[sha1]=0x0351c94aaf487ee3559a722446865b7ae0f3b7cc, not stripped Here the R scripts: /opt/sdr/report/var/FastRWeb $ ls -lrt total 16 drwxr-xr-x 2 sdr sdr 4096 Feb 18 00:08 web drwxr-xr-x 2 sdr sdr 4096 Feb 18 00:08 tmp drwxr-xr-x 2 sdr sdr 4096 Feb 19 14:27 code srw-rw-rw- 1 sdr sdr 0 Feb 19 14:27 socket =>> drwxr-xr-x 2 sdr sdr 4096 Feb 19 14:28 web.R all R scripts will go here web.R directory. stefan
on 2013-02-19 17:22
Sounds like you ought to try writing a wrapper script ending in .cgi in the cgi dir that grabs the query string and hands the job off to the R executable. Not sure if R is required in the cgi-bin directory. You might have to enable symlinking out for it to work. On Tue, Feb 19, 2013 at 9:49 AM, Stefan Parvu <sparvu@systemdatarecorder.org
on 2013-02-19 17:41
On 11:22 Tue 19 Feb , Harold Sinclair wrote: > Sounds like you ought to try writing a wrapper script ending in .cgi in the > cgi dir that grabs the query string and hands the job off to the R > executable. Not sure if R is required in the cgi-bin directory. You might > have to enable symlinking out for it to work. yeah not sure how to do it. FastRWeb tell us: " FastRWeb consists of several parts: Webserver-to-R pipeline, consisting of either a thin CGI or a PHP client connecting to Rserve which sources and runs the R script. The CGI client is called Rcgi and is compiled as part of the package. The PHP client is part of Rserve in the clients section. " So Im on option 1: CGI. The client will be this binary which somehow needs to be executed for each R script. I placed the Rcgi under cgi.bin directory and rename it as R.cgi. If I call directly: http://localhost:9001/cgi-bin/R.cgi the browser returns: Error: no function or path specified. http://localhost:9001/cgi-bin/R.cgi/foo.png?n=100 I see under error log: 2013/02/19 18:39:53 [error] 2847#0: *56 open() "/opt/sdr/report/docroot/cgi-bin/R.cgi/foo.png" failed (20: Not a directory), client: 127.0.0.1, server: sdrrep, request: "GET /cgi-bin/R.cgi/foo.png?n=100 HTTP/1.1", host: "localhost:9001" stefan
on 2013-02-19 17:44
> So Im on option 1: CGI. The client will be this binary which somehow needs to be > executed for each R script. I placed the Rcgi under cgi.bin directory and rename it > as R.cgi. > and I forgot to mention for CGI Im using FcgiWrap: http://nginx.localdomain.pl/wiki/FcgiWrap stefan
on 2013-02-19 18:24
On Tue, Feb 19, 2013 at 12:47:23PM +0000, Stefan Parvu wrote: Hi there, This location: > location ~ ^/cgi-bin/.*\.cgi$ { will only match some requests that end in ".cgi" (before the ?, if that applies). What you possibly want is a separate location just for your "R" requests. Something like (untested by me!) location ^~ /cgi-bin/R/ { } in which you have your "fastcgi_pass" directive, plus whatever "fastcgi_param" directives you need to make it work. That is *probably* fastcgi_param REQUEST_URI $request_uri; fastcgi_param QUERY_STRING $query_string; fastcgi_param SCRIPT_FILENAME $document_root/cgi-bin/R; but the exact details depend on what your fastcgi server wants. (You may want to set PATH_INFO, if your application uses that.) See http://nginx.org/r/location for the details of which one location{} is chosen for each request, and then see the fastcgi documentation to decide exactly what params you need. Usually, SCRIPT_FILENAME is "the file on the filesystem that the fastcgi server should execute"; and other things are "stuff that the fastcgi server or the application can use to decide what to do". > and Im using fcgiwrap from http://nginx.localdomain.pl/wiki/FcgiWrap. > CGI scripts work fine but Im not able to any R scripts probable due > R being not correctly called via nginx.conf ... In this case, yes. Your nginx configuration was such that your requests for "R" were not being sent to the fastcgi server. > I am trying something like: http://localhost/cgi-bin/R/foo.png?n=500 > and R is a binary file under cgi-bin directory which should call > FastRWeb ... Provided that the fastcgi server is able to run whatever file you name in SCRIPT_FILENAME, and has access to whatever other params it cares about, something like the above configuration has a chance of working. f -- Francis Daly francis@daoine.org
on 2013-02-20 11:02
> > Something like (untested by me!) > location ^~ /cgi-bin/R/ { } > yep correct. I do have now on cgi-bin directory a binary file called: R. I did change my nginx.conf to have a new location definition for the R calls, like here: location ~ ^/cgi-bin/R$ { gzip off; fastcgi_pass unix:/opt/sdr/report/ws/fastcgi_temp/nginx-fcgi.sock; fastcgi_param REQUEST_METHOD $request_method; fastcgi_param SCRIPT_FILENAME /opt/sdr/report/docroot$fastcgi_script_name; fastcgi_param PATH_INFO $fastcgi_path_info; fastcgi_param REQUEST_URI $request_uri; fastcgi_param DOCUMENT_URI $document_uri; fastcgi_param DOCUMENT_ROOT /opt/sdr/report/docroot; fastcgi_param SERVER_PROTOCOL $server_protocol; fastcgi_param REMOTE_ADDR $remote_addr; fastcgi_param REMOTE_PORT $remote_port; fastcgi_param SERVER_ADDR $server_addr; fastcgi_param SERVER_PORT $server_port; fastcgi_param SERVER_NAME $server_name; } This works if I put in my browser: http://localhost:9001/cgi-bin/R I get some error in the browser but it does seem to work since I did not input any parameters to R call. But when I try: http://localhost:9001/cgi-bin/R/foo?n=50 this returns with same error that there is no such directory, seems somehow the request it is not passed via CGI to FastWebR. 2013/02/20 11:52:01 [error] 3637#0: *9 open() "/opt/sdr/report/docroot/cgi-bin/R/foo" failed (20: Not a directory), client: 127.0.0.1, server: sdrrep, request: "GET /cgi-bin/R/foo?n=50 HTTP/1.1", host: "localhost:9001" > In this case, yes. Your nginx configuration was such that your requests > for "R" were not being sent to the fastcgi server. And still they are not passed correctly. something still messed up with my nginx.conf you can see entire nginx.conf here: http://www.systemdatarecorder.org/nginx.conf Stefan
on 2013-02-20 14:25
On Wed, Feb 20, 2013 at 10:00:04AM +0000, Stefan Parvu wrote: > > Something like (untested by me!) > > location ^~ /cgi-bin/R/ { } > yep correct. I do have now on cgi-bin directory a binary file called: R. > I did change my nginx.conf to have a new location definition for the > R calls, like here: > > location ~ ^/cgi-bin/R$ { "~" means "regex". "^" means "start of string". "$" means "end of string". This location will only match requests that are /cgi-bin/R or /cgi-bin/R?something and not /cgi-bin/R/something > But when I try: http://localhost:9001/cgi-bin/R/foo?n=50 > this returns with same error that there is no such directory, seems somehow > the request it is not passed via CGI to FastWebR. Yes, that's what you configured. What happens when you test exactly what was suggested? f -- Francis Daly francis@daoine.org
on 2013-02-20 21:30
> > /cgi-bin/R/something > yep. silly me, I do have a location for all /cgi-bin/R/ calls, like: location ~ ^/cgi-bin/R/ { gzip off; fastcgi_pass unix:/opt/sdr/report/ws/fastcgi_temp/nginx-fcgi.sock; fastcgi_index index.cgi; fastcgi_param SCRIPT_FILENAME /opt/sdr/report/docroot/$fastcgi_script_name; fastcgi_param PATH_INFO $fastcgi_path_info; fastcgi_param QUERY_STRING $query_string; fastcgi_param REQUEST_METHOD $request_method; fastcgi_param CONTENT_TYPE $content_type; fastcgi_param CONTENT_LENGTH $content_length; fastcgi_param REQUEST_URI $request_uri; fastcgi_param DOCUMENT_URI $document_uri; fastcgi_param DOCUMENT_ROOT /opt/sdr/report/docroot; } and another one for anything *.cgi: location ~ ^/cgi-bin/.*\.cgi$ { gzip off; fastcgi_pass unix:/opt/sdr/report/ws/fastcgi_temp/nginx-fcgi.sock; fastcgi_read_timeout 5m; fastcgi_index index.cgi; #fastcgi_buffers 8 4k; # # You may copy and paste the lines under or use include directive # include /etc/nginx/nginx-fcgi.conf; # In this example all is in one file ... } since under my /cgi-bin/ I can have lots of cgi scripts and the executable R cgi script. Testing any calls for /cgi-bin/R/foo returns: Cannot get script name, are DOCUMENT_ROOT and SCRIPT_NAME (or SCRIPT_FILENAME) set and is the script executable? Cannot get script name, are DOCUMENT_ROOT and SCRIPT_NAME (or SCRIPT_FILENAME) set and is the script executable? Im trying to see if fastcgi_split_path_info might help anything. stefan
on 2013-02-20 22:44
On Wed, Feb 20, 2013 at 08:28:27PM +0000, Stefan Parvu wrote: > location ~ ^/cgi-bin/R/ { That will match anything starting with /cgi-bin/R/, which is (most of) what you want. These requests will... > fastcgi_pass unix:/opt/sdr/report/ws/fastcgi_temp/nginx-fcgi.sock; be sent to the fastcgi server. Now, for all of these requests, you want to tell the fastcgi server to use the file /opt/sdr/report/docroot/cgi-bin/R. So: > fastcgi_index index.cgi; you don't need that, since it will never apply; and > fastcgi_param SCRIPT_FILENAME /opt/sdr/report/docroot/$fastcgi_script_name; that should be something that expands to /opt/sdr/report/docroot/cgi-bin/R. Which is probably $document_root/cgi-bin/R; you can use whatever matches exactly that filename. $fastcgi_script_name does not have the correct value by default, in this case. > fastcgi_param PATH_INFO $fastcgi_path_info; If your application uses PATH_INFO, then you'll want to set it something like that. I don't think that $fastcgi_path_info actually has a value by default, though. > fastcgi_param QUERY_STRING $query_string; > fastcgi_param REQUEST_METHOD $request_method; > fastcgi_param CONTENT_TYPE $content_type; > fastcgi_param CONTENT_LENGTH $content_length; > fastcgi_param REQUEST_URI $request_uri; > fastcgi_param DOCUMENT_URI $document_uri; > fastcgi_param DOCUMENT_ROOT /opt/sdr/report/docroot; They are all fairly standard; probably only the first and last matter, but it depends on your fastcgi server and your application. The last one would usually be written to use $document_root, but anything that ends up with the correct value is good. Note that your fastcgi server, from the logs you provide, either wants SCRIPT_FILENAME to be correct, or DOCUMENT_ROOT and SCRIPT_NAME to be correct; and you don't provide a SCRIPT_NAME. That may not matter when SCRIPT_FILENAME points to the R binary. > Testing any calls for /cgi-bin/R/foo returns: > Cannot get script name, are DOCUMENT_ROOT and SCRIPT_NAME (or SCRIPT_FILENAME) set and is the script executable? > Cannot get script name, are DOCUMENT_ROOT and SCRIPT_NAME (or SCRIPT_FILENAME) set and is the script executable? From the above config, SCRIPT_FILENAME was probably /opt/sdr/report/docroot/cgi-bin/R/foo, which is not an executable file. > Im trying to see if fastcgi_split_path_info might help anything. Yes. http://nginx.org/r/fastcgi_split_path_info It will change the values of $fastcgi_script_name and $fastcgi_path_info. f -- Francis Daly francis@daoine.org
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