User Access

EMSL's Response

Safety is one of EMSL's goals. EMSL strives to balance effective training while adhering to DOE and PNNL training requirements. Within the last year, training requirements at PNNL have changed, resulting in many users having to take the same training as staff or vendors. EMSL is working with PNNL to reassess and revise the training required by EMSL users. EMSL is also working on adding a training tab to the new EMSL User Portal, which will allow for easier way to access and track training.

EMSL's Response

In an effort to evolve as a world-class national scientific user facility and better focus our scientific direction, EMSL implemented changes to the user policy and proposal processes. On November 1, 2006, EMSL implemented a new Call for Proposals structure. A user policy update memo describing these changes was sent to participants on open proposals on October 27, 2006. We understand your frustration during this time of process change. Proposals may be submitted in response to specific calls for proposals at specific times of the year, or in response to the Open Call at any time during the year. Resource allocation is dependent on the nature of the proposal and length of access time. In order to ensure fairness, and track usage of resources in the EMSL, ALL work in the EMSL requires an active proposal. The EMSL website was updated again in attempt to make the user proposal process clearer. The new webpage and policy describing the basic requirements for a proposal and the review criteria and process should make the procedure more explanatory.

EMSL's Response

The new proposal process was initiated to ensure that access to EMSL was an open and transparent process. Proposals go through peer review to determine if it is an appropriate use of EMSL and to ensure that the research carried out at EMSL is well aligned with the facilities mission, science themes, resources, operation envelope, and instrument/staff capabilities. Proposals in response to any other call other than Open, are reviewed and ranked against each other (note Open call proposals under go peer review too). EMSL received almost 300 proposals in response to the 2007 Science Theme Call for Proposals. It takes a few months to review, process, and allocate this many proposals.

EMSL's Response

Recently, EMSL has issued charging guidance for EMSL user facility staff – note only accessible by PNNL staff.

EMSL's Response

EMSL has recently rolled out the EMSL User Portal, which allows users to see the status of all their proposals. Reviews of your proposals (since the external review system was implemented) are now available. Users can upload proposal summaries and associated publications.

EMSL's Response

We are in the process of procuring a shielded 600-MHz NMR system that will be equipped with liquid chromatography and flow capabilities as well as automated sample introduction. These capabilities will be primarily dedicated to metabolomics studies. The system will also be equipped with at least one cryogenic probe and will be switchable between NMR sample tube and flow modes.

EMSL's Response

Unfortunately, we had some scheduling lapses/overlap while transitioning from our 6-month HFMRF-specific calls to EMSL's annual Science Theme call for proposals, which caused some problems for our users. We will be re-examining how we schedule users based on the new annual schedule in order to improve time allotment on oversubscribed systems. Our staff also will more effectively communicate with our users to encourage scheduling soon after time is allotted and will provide incentives to those who do schedule early. We will also regularly be evaluating alternative scheduling models.

EMSL's Response

This fall, EMSL will purchase a tandem mass spectrometer with electron transfer dissociation (ETD) capability that will be available to users in early Calendar Year 2008. The ETD capability will allow for increased effective identification of post translational modifications, a key piece of information essential to understanding activation of proteins in cells. In addition, a new linear ion trap will be procured to replace an older three-dimensional ion trap, bringing improved dynamic range and cycle time for acquiring spectra and improving the quality of proteomics analyses performed at EMSL. Finally, a data storage server will be purchased that will enable effect use of the instrument.

EMSL's Response

Researchers are increasingly seeking time on EMSL's supercomputer. The MSCF has chosen to accept more proposals, often granting smaller time allocations, rather than accepting fewer proposals with full time allocations. Significantly more time is expected to be allocated to continuing projects when EMSL's new supercomputer becomes operational in Spring 2008.

EMSL's Response

The MSCF focuses on providing the right hardware, software, and consultation to scientists who integrate theory and experiment to solve complex computational chemistry, biochemistry, and environmental problems facing DOE and the nation. Our current policy is to give priority to such complex research projects that use a large number of processors. As a result, smaller jobs requiring long execution times tend to wait longer in the queue. We will soon be revisiting our queuing policy in anticipation of our new supercomputer to ensure that our users in the future are given balanced support for both large-scale and small-scale jobs associated with EMSL science theme projects.

EMSL's Response

Currently, 16 processors are available during regular business hours (not weekends) for quick tests with a 30-minute maximum run time. When our new supercomputer becomes operational in Spring 2008, more processors will be available for quick tests. Interactive jobs can be run at any time when the processors are available. Use the "window" command to see how many idle processors are available.

EMSL's Response

PNNL is working to upgrade its internet hardware and software to improve speed and security. In addition, network "down times" are typically scheduled to minimize disruption but still may impact users in other time zones. Finally, the arrival and subsequent operation of EMSL's new supercomputer, slated for Spring 2008, will also help alleviate issues with availability and performance. The system will have greater capacity but a similar balance of processor speed, memory bandwidth, and local scratch, and is expected to have about 5 to 10 times the current capacity of MPP2.

EMSL's Response

Copying very large files on local scratch disks to the home directory may take too long to complete. In such cases, the /dtemp (Lustre) file system should be used for files that will need to be saved. Local scratch should be used for files that do not need to be saved. Large output files on /dtemp can then be copied to NWfs for storage.

EMSL's Response

Large files can be more efficiently copied to remote locations using an ftp protocol instead of scp. Please refer to NWfs Access for more details.

EMSL's Response

The software stack on MPP2 was the original kernel from 2003 and was so old that new versions of compilers and debugging tools could not work. We tested the new stack on a small test cluster and confirmed our supported software codes would run. Tuning issues like default buffer sizes and environment settings were not identified until the new stack was running on the full computer. The module command was developed to provide correct paths to compatible commands, compilers, libraries and environment variable settings. Users who make files that contain full path links to compilers and/or libraries will usually have problems due to incompatible combinations.

EMSL's Response

The performance problems observed have been resolved, and the CCSD(T) is now working as fast as expected by our users. We apologize for the lengthy resolution time; it was very difficult to find the cause and to fix the issue. Efforts are ongoing to further improve the performance of the code.

EMSL's Response

The NWChem developer team is continuously making scalability improvements. Funding has been obtained to further develop NWChem to scale to tens of thousands of processors for plane-wave DFT, TCE, and MD calculations. Some of the improvements will be ready at the next release and when the new supercomputer becomes available. Our team is also working with Oak Ridge National Laboratory to make sure NWChem performs on the XT4 leadership computing facility. We are also expanding the plane-wave capabilities; some of the improvements will be available in the next release. We are also working continuously to update and improve the NWChem user manual. Users should feel free to provide specific feedback to help us to further improve their experience using NWChem.

EMSL's Response

The ESB Facility will be adding two major capabilities in Fiscal Year 2008: a micro X-ray diffractometer and micro-fluidics capability. Toward procurement of a high-end fluorescence confocal microscope, we have evaluated commercially available systems but have not yet found the ideal combination of capabilities in a single microscope. Meanwhile, we are in the process of evaluating what additional capabilities are needed to upgrade our in-house-developed confocal microscope, and we welcome specific input from users on capabilities their research would require in this area.

In addition, we recognize that additional capabilities require replacement, such as the fluorimeter, which we hope to replace next fiscal year.

The capabilities of our Subsurface Flow and Transport Laboratory (SFTL) are currently constrained by laboratory space. However, as part of the ongoing reorganization of facilities and capabilities an opportunity may exist to move the SFTL into a larger space. At this time we are considering both expanding the dual gamma capability by mounting the flow cells on a carousel and adding an x-ray capability.

EMSL's Response

Recent upgrades and new capabilities in the INSF include:

X-ray photon spectrometer: EMSL is purchasing a new XPS system that consists of UPS and C-60 depth profiling in addition to the XPS capability. This new system is expected to arrive at EMSL in August/September and will be available for users in early Fiscal Year 2008.

Focused ion beam/scanning electron microscopy capability update: We are in the process of installing the instrumentation. Installation and testing are expected to be completed within next 2 to 3 months. We expect the capability to be fully operable for users in November/December.

Transmission electron microscope capability with heating and cooling: The following four options are available at EMSL regarding TEM capability with heating and cooling:

1. Recently, we established the cryo-TEM capability with cryostage and tomography. This capability is fully operational and available to users.
2. We are developing a high-resolution, aberration-corrected TEM with heating capability, a monochromator, and an environmental cell. This capability will incorporate z contrast TEM imaging using high angular annular detectors. Development of this capability is expected to be completed by the end of next fiscal year.
3. We are also developing anaerobic sample introduction stage, cryo-stage, and heating capabilities for our JEOL 2010 microscope. The anaerobic sample introduction stage has been recently incorporated, with the other capabilities still under development.
4. The new focused ion beam/scanning electron microscopy, as described above.

General catalyst testing: The INSF houses several catalyst test stands, catalysis reactors, and catalyst characterization capabilities.

Electrochemical impedance spectroscopy We are developing this capability, which is expected to be functional in October.

Data acquisition software upgrade for TEM: We are upgrading the data acquisition system for our high-resolution JEOL 2010 microscope. Development of this new data acquisition system, a much more user friendly, PC-based system, is expected to be completed by September 30, 2007.

Low-temperature STM/NC AFM: This capability is listed in EMSL's recapitalization plan and it is expected to be available for users in 2010.

EMSL's Response

During Fiscal Year 2007, $160K in operation supported equipment upgrades in CPCS. These included modification of the multi-photon confocal microscope for new molecular and cellular imaging capabilities, acquisition of a new optical system for photochemistry of molecules on surfaces within a UHV chamber, purchase of a close loop piezo translation stage for aligning cell samples with nanometer precision, and purchase of STM image processing software for analysis of diffusion dynamics of adsorbates on surfaces. Plans for new capital investments for major CPCS instrument systems are under review.