Attention

This documentation is under active development, meaning that it can change over time as we refine it. Please email help@massive.org.au if you require assistance, or have suggestions to improve this documentation.

DRAFT Instructions for MX2 Eiger Users

M3 is available to users associated with MASSIVE partners for transferring and processing Eiger data. Please follow these instructions to get started.

Access to MX data through CAP projects on M3

MASSIVE will create a mirror of MX CAP projects. This project will allow CAP researchers to access MX CAP data, using a documented set of instructions, for the period of the CAP and up to a period after. We intend these projects for data access only and we would like to suggest that you create a dedicated research lab-focused and long-lived project for the bulk of your data processing.

To check which CAP projects you are part of, please go to https://hpc.erc.monash.edu.au/karaage and log in using an Australian Access Federation (AAF) account. After logging in successfully, please select the “Projects” tabs on the left panel; you will find a list of your projects under “Projects I am a member of” section.

CAP members must request access. Please follow these instructions to create an account and request access to an existing CAP project but replace m3earlyadopters with your project code: http://docs.massive.org.au/M3/requesting-an-account.html

Important

CAP leaders: The invite function does not currently work. Please DO NOT send invites to your project members; instruct them to use the instructions on this page.

Create a research lab project for your research lab

M3 use is organised into projects that are lead by a project lead. The project lead is responsible for managing users within the project and communicating with the MASSIVE team about allocations and project reporting. We recommend that M3 projects are lead by research laboratory leads.

M3 projects are not the same as CAP projects; research laboratory leads must apply for a separate M3 project to process MX data.

If your group already has an M3 project, proceed directly to the next section.

To request an M3 project:

  1. Fill out the following project request form

  2. The MASSIVE team will email your project team members with instructions on how to create an account and join your project.

Important

Creating projects and user accounts takes around 48 hours, or 2 business days. If you do not receive a confirmation email within 48 business hours, please contact the MASSIVE help desk at help@massive.org.au

Getting started on M3

Please look over http://docs.massive.org.au/ to get acquainted with the M3 system.

Alternatively, the MASSIVE team are happy to schedule on-boarding sessions for lab groups. Please email help@massive.org.au to organise a session.

Connecting to M3

Connect to M3 and start a shell/terminal session. This can be done in one of three ways. Please see Connecting to M3 for details on each of these options.

Users who have logged in using a desktop session will need to launch a terminal. This can be done by doubling clicking on the terminal icon, shown below.

In the terminal that you have just opened, enter:

module load xds/slurmenabled

Transfer your MX data

Begin by connecting to m3.

Transferring data from the Australian Synchrotron is a two step process. The first step is to setup passwordless access for your M3 account to access the AS data server (this needs to be done only once). The second step is to synchronise the appropriate data sets from AS to your M3 account.

Setting up passwordless access

Use the command

ssh-copy-id <username>@sftp.synchrotron.org.au

where username is your Australian Synchrotron username (probably an email address) Note that this command probably includes the @ symbol twice, once in the AS username (which is an email address) and once in the @sftp.synchtron.org.au part.

You will then be prompted to enter your Australian Synchrotron password (not your M3 password).

Transferring your data

If you wish to synchronise only once (because you know the data is not changing) use the flag –once as in the example below

syncsync.py --username=<username> --path=<epn> --once

For example, the two commands below are used to transfer user1’s‘ frames and homes folders from epn 123456a to M3 once

syncsync.py --username=user1@example.com --path=123456a/frames/user1 --once
syncsync.py --username=user1@example.com --path=123456a/homes/user1 --once

If you need to do continuous data sync, because you are still expecting more data from the instrument, run the command without the –once tag

module load xds/slurmenabled
syncsync.py --username=user1@example.com --path=123456a/frames/user1
syncsync.py --username=user1@example.com --path=123456a/homes/user1

These commands will continuously loop looking for changes in the AS data store and synchronising the homes and frames folders to M3.

For more general information on transferring data, please see Copying files to and from M3

If you have data stored on a portable hard drive and are finding it difficult to upload your data to M3, please email help@massive.org.au to organise a time to drop off your hard drive. We will then upload the data to M3 for you.

Important

The data transfer may take around 10 to 12 hours depending on the size of dataset. We recommend the use of tmux before running the commands to start the transfer. Please email help@massive.org.au if you need help with running tmux.

Process your data

Change to the directory that contains your data for XDS processing:

cd <path>

Examine the XDS.INP file in this directory, and verify that these values are present to take maximum advantage of M3:

MAXIMUM_NUMBER_OF_JOBS=4
MAXIMUM_NUMBER_OF_PROCESSORS=24
LIB= /usr/local/xds/20170302/lib/dectris-neggia-centos7.so

You might also wish to include these values as recommended by the MX Beamline scientists

JOB=ALL
FRIEDEL\'S_LAW=FALSE

If there is no XDS.INP file present, please consult your lab head or colleagues.

Fix the symlink to the img folder:

unlink img
ln -s <path-to-data> img

Run the command xds_par and wait for the process to finish. You will be returned to your terminal prompt. The output of the command is displayed on the terminal screen and is also stored in xds_stdout file in the same folder where xds_par was run.

Known Issues

Cannot open or read filename.tmp error

The following error may appear when you are attempting to process data:

!!! ERROR !!! CANNOT OPEN OR READ FILE LP_01.tmp

Presumably, the independent jobs supposed to have been started
in the COLSPOT step have not run properly. This could be due
to incomplete installation of XDS where some of the executables
of the package are not included in the search path.

!!! ERROR !!! CANNOT OPEN OR READ "mcolspot.tmp"

To fix this error, run the module purge command, followed by reloading the xds module:

module purge
module load xds/slurmenabled
xds_par