MPI cannot execute with machine file or hosts from SSH using JSch exec channel [duplicate] - ssh

Question

I have a piece of code which connects to a Unix server and executes commands.
I have been trying with simple commands and they work fine.
I am able to login and get the output of the commands.
I need to run an Ab-initio graph through Java.
I am using the air sandbox run graph command for this.
It runs fine, when I login using SSH client and run the command. I am able to run the graph. However, when I try to run the command through Java it gives me a "air not found" error.
Is there any kind of limit on what kind of Unix commands JSch supports?
Any idea why I'm not able to run the command through my Java code?
Here's the code:
public static void connect(){
try{
JSch jsch=new JSch();
String host="*****";
String user="*****";
String config =
"Host foo\n"+
" User "+user+"\n"+
" Hostname "+host+"\n";
ConfigRepository configRepository =
com.jcraft.jsch.OpenSSHConfig.parse(config);
jsch.setConfigRepository(configRepository);
Session session=jsch.getSession("foo");
String passwd ="*****";
session.setPassword(passwd);
UserInfo ui = new MyUserInfo(){
public boolean promptYesNo(String message){
int foo = 0;
return foo==0;
}
};
session.setUserInfo(ui);
session.connect();
String command="air sandbox run <graph-path>";
Channel channel=session.openChannel("exec");
((ChannelExec)channel).setCommand(command);
channel.setInputStream(null);
((ChannelExec)channel).setErrStream(System.err);
InputStream in=channel.getInputStream();
channel.connect();
byte[] tmp=new byte[1024];
while(true){
while(in.available()>0){
int i=in.read(tmp, 0, 1024);
if(i<0)break;
page_message=new String(tmp, 0, i);
System.out.print(page_message);
}
if(channel.isClosed()){
if(in.available()>0) continue;
System.out.println("exit-status: "+channel.getExitStatus());
break;
}
try{Thread.sleep(1000);}catch(Exception ee){}
}
channel.disconnect();
session.disconnect();
}
catch(Exception e){
System.out.println(e);
}
}
public static void main(String arg[]){
connect();
}
public String return_message(){
String ret_message=page_message;
return ret_message;
}
public static abstract class MyUserInfo
implements UserInfo, UIKeyboardInteractive{
public String getPassword(){ return null; }
public boolean promptYesNo(String str){ return false; }
public String getPassphrase(){ return null; }
public boolean promptPassphrase(String message){ return false; }
public boolean promptPassword(String message){ return false; }
public void showMessage(String message){ }
public String[] promptKeyboardInteractive(String destination,
String name,
String instruction,
String[] prompt,
boolean[] echo){
return null;
}
}

Answer 1

The "exec" channel in the JSch (rightfully) does not allocate a pseudo terminal (PTY) for the session. As a consequence a different set of startup scripts is (might be) sourced (particularly for non-interactive sessions, .bash_profile is not sourced). And/or different branches in the scripts are taken, based on absence/presence of the TERM environment variable. So the environment might differ from the interactive session, you use with your SSH client.
So, in your case, the PATH is probably set differently; and consequently the air executable cannot be found.
To verify that this is the root cause, disable the pseudo terminal allocation in your SSH client. For example in PuTTY, it's Connection > SSH > TTY > Don't allocate a pseudo terminal. Then, go to Connection > SSH > Remote command and enter your air ... command. Check Session > Close window on exit > Never and open the session. You should get the same "air not found" error.
Ways to fix this, in preference order:
Fix the command not to rely on a specific environment. Use a full path to air in the command. E.g.:
/bin/air sandbox run <graph-path>
If you do not know the full path, on common *nix systems, you can use which air command in your interactive SSH session.
Fix your startup scripts to set the PATH the same for both interactive and non-interactive sessions.
Try running the script explicitly via login shell (use --login switch with common *nix shells):
bash --login -c "air sandbox run sandbox run <graph-path>"
If the command itself relies on a specific environment setup and you cannot fix the startup scripts, you can change the environment in the command itself. Syntax for that depends on the remote system and/or the shell. In common *nix systems, this works:
String command="PATH=\"$PATH;/path/to/air\" && air sandbox run <graph-path>";
Another (not recommended) approach is to force the pseudo terminal allocation for the "exec" channel using the .setPty method:
Channel channel = session.openChannel("exec");
((ChannelExec)channel).setPty(true);
Using the pseudo terminal to automate a command execution can bring you nasty side effects. See for example Is there a simple way to get rid of junk values that come when you SSH using Python's Paramiko library and fetch output from CLI of a remote machine?
For a similar issues, see
Certain Unix commands fail with "... not found", when executed through Java using JSch even with setPty enabled
Commands executed using JSch behaves differently than in SSH terminal (bypasses confirm prompt message of "yes/"no")
JSch: Is there a way to expose user environment variables to "exec" channel?
Command (.4gl) executed with SSH.NET SshClient.RunCommand fails with "No such file or directory"

Answer 2

you could try to find out where "air" resides with
whereis air
and then use this outcome.
something like
/usr/bin/air sandbox run graph

Answer 3

You can use an ~/.ssh/environment file to set your AB_HOME and PATH variables.