Commit c4a41a23 authored by Stefano Alberto Russo's avatar Stefano Alberto Russo
Browse files

Fixed bug that prevented some containers to run due to write permission issues in home.

parent 17399407

services/webapp/code/rosetta/core_app/computing_managers.py

+8 −8
Original line number Diff line number Diff line
@@ -208,8 +208,8 @@ class RemoteComputingManager(ComputingManager): 
            run_command  = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)

            run_command += '/bin/bash -c \'"wget {}/api/v1/base/agent/?task_uuid={} -O \$HOME/agent_{}.py &> /dev/null && export BASE_PORT=\$(python \$HOME/agent_{}.py 2> \$HOME/{}.log) && '.format(webapp_conn_string, task.uuid, task.uuid, task.uuid, task.uuid)

            run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT && {} '.format(authstring)

            run_command += 'rm -rf /tmp/{}_data && mkdir /tmp/{}_data &>> \$HOME/{}.log && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid, task.uuid) 

            run_command += 'exec nohup singularity run {} --pid --no-home --home=/home/metauser --workdir /tmp/{}_data --containall --cleanenv '.format(binds, task.uuid)

            run_command += 'rm -rf /tmp/{}_data && mkdir -p /tmp/{}_data/tmp &>> \$HOME/{}.log && mkdir -p /tmp/{}_data/home &>> \$HOME/{}.log && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid, task.uuid, task.uuid, task.uuid) 

            run_command += 'exec nohup singularity run {} --pid --no-home --home=/home/metauser --workdir /tmp/{}_data/tmp -B/tmp/{}_data/home:/home/metauser --containall --cleanenv '.format(binds, task.uuid, task.uuid)

            

            # Set registry

            if task.container.registry == 'docker_local':
@@ -366,8 +366,8 @@ class SlurmComputingManager(ComputingManager): 
            run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)

            run_command += '\'bash -c "echo \\"#!/bin/bash\nwget {}/api/v1/base/agent/?task_uuid={} -O \$HOME/agent_{}.py &> \$HOME/{}.log && export BASE_PORT=\\\\\\$(python \$HOME/agent_{}.py 2> \$HOME/{}.log) && '.format(webapp_conn_string, task.uuid, task.uuid, task.uuid, task.uuid, task.uuid)

            run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\\\\\\$BASE_PORT && {} '.format(authstring)

            run_command += 'rm -rf /tmp/{}_data && mkdir /tmp/{}_data &>> \$HOME/{}.log && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid, task.uuid)

            run_command += 'exec nohup singularity run {} --pid --no-home --home=/home/metauser --workdir /tmp/{}_data --containall --cleanenv '.format(binds, task.uuid)

            run_command += 'rm -rf /tmp/{}_data && mkdir -p /tmp/{}_data/tmp &>> \$HOME/{}.log && mkdir -p /tmp/{}_data/home &>> \$HOME/{}.log && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid, task.uuid, task.uuid, task.uuid)

            run_command += 'exec nohup singularity run {} --pid --no-home --home=/home/metauser --workdir /tmp/{}_data/tmp -B/tmp/{}_data/home:/home/metauser --containall --cleanenv '.format(binds, task.uuid, task.uuid)

            

            # Double to escape for Pythom, six for shell (double times three as \\\ escapes a single slash in shell)
@@ -525,15 +525,15 @@ class RemotehopComputingManager(ComputingManager): 
                if setup_command:

                    run_command += setup_command + ' && '

                run_command += '\'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT && {} '.format(authstring)

                run_command += 'rm -rf /tmp/{}_data && mkdir /tmp/{}_data &>> \$HOME/{}.log && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid, task.uuid)

                run_command += 'exec nohup singularity run {} --pid --no-home --home=/home/metauser --workdir /tmp/{}_data --containall --cleanenv '.format(binds, task.uuid)

                run_command += 'rm -rf /tmp/{}_data && mkdir -p /tmp/{}_data/tmp &>> \$HOME/{}.log && mkdir -p /tmp/{}_data/home &>> \$HOME/{}.log && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid, task.uuid, task.uuid, task.uuid)

                run_command += 'exec nohup singularity run {} --pid --no-home --home=/home/metauser --workdir /tmp/{}_data/tmp -B/tmp/{}_data/home:/home/metauser --containall --cleanenv '.format(binds, task.uuid, task.uuid)

            else:

                run_command += ' : && ' # Trick to prevent some issues in exporting variables                

                if setup_command:

                    run_command += setup_command + ' && '

                run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT={} && {} '.format(task.port, authstring)

                run_command += 'rm -rf /tmp/{}_data && mkdir /tmp/{}_data &>> \$HOME/{}.log && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid, task.uuid)

                run_command += 'exec nohup singularity run {} --pid --no-home --home=/home/metauser --workdir /tmp/{}_data --containall --cleanenv '.format(binds, task.uuid)

                run_command += 'rm -rf /tmp/{}_data && mkdir -p /tmp/{}_data/tmp &>> \$HOME/{}.log && mkdir -p /tmp/{}_data/home &>> \$HOME/{}.log && chmod 700 /tmp/{}_data && '.format(task.uuid, task.uuid, task.uuid, task.uuid, task.uuid, task.uuid)

                run_command += 'exec nohup singularity run {} --pid --no-home --home=/home/metauser --workdir /tmp/{}_data/tmp -B/tmp/{}_data/home:/home/metauser --containall --cleanenv '.format(binds, task.uuid, task.uuid)

             

            # Set registry

            if task.container.registry == 'docker_local':