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Can GWB (professional verison) be copied to virtual machine or super computer?


HUAN
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Hi, everyone:

Our group has a professional verison of GWB. But the simulation speed is too slow when I use X1t. For example, it may requires more than 3 days or more to finish one run. Sometimes, the simulation calculation just terminate at 30%, or even 90%. So, I think this maybe due to the simulation computer is too old.

So I want to copy the GWB software to the virtual machine or super computer in our university. Can anyone tell me that is it feasible? 

If it is not feasible, I want to buy a new workstation. Can anyone give me some recommendations about the computer parameters?

Our current computer:

processor: intel(R) Xeon(R) CPU E5-1630 v3 @ 3.70GHz 3.70GHz

Installed memory (RAM): 32.0 GB

System type: 64-bit operating system, x64-based processor

 

Thanks for help.

Huan

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Hello Huan,

Thank you for providing the information on your machine. With these specs, I think your computer isn't the primary issue here. Running a complicated Reactive Transport Model can often take a little bit of time to complete but if you find it to be too slow, it can be related to other issues. Here are a couple of things to check:

1) Check if one or more kinetic reactant reaction rates are too fast. If your reaction rates are really fast, the program will select really small time steps for your simulation. In that case, your run might take a lot more time. If you find that there are reactions that are occurring extremely fast relative to the time scale of your interest, you might consider using an equilibrium approach for those reactants. 

2) Sometimes runs may take a long time if you are modeling complex biological reactions. In that case, you might want to adjust your model to use the reaction rate evaluated at the old time level, a fully explicit approach. This is controlled by the variable theta, which can range from 0 to 1, where 0 is the full weighting of the rate at the old time level and 1 is fully weighting at the new time level. By default, X1t, X2t, and React are set to an use an average of the kinetic rates at the old and new time level with theta set at 0.6. To change to a fully explicit model, go to Config --> Stepping -> theta = 0. You can find more information regarding theta in 4.1 (Setting kinetic reactions) in the GWB Reaction Modeling Guide. 

If these suggestions didn't help with improving your run speed, please post your input file along with any custom databases so we can take a closer look. 

Hope this helps,
Jia Wang

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52 minutes ago, Jia Wang said:

Hello Huan,

Thank you for providing the information on your machine. With these specs, I think your computer isn't the primary issue here. Running a complicated Reactive Transport Model can often take a little bit of time to complete but if you find it to be too slow, it can be related to other issues. Here are a couple of things to check:

1) Check if one or more kinetic reactant reaction rates are too fast. If your reaction rates are really fast, the program will select really small time steps for your simulation. In that case, your run might take a lot more time. If you find that there are reactions that are occurring extremely fast relative to the time scale of your interest, you might consider using an equilibrium approach for those reactants. 

2) Sometimes runs may take a long time if you are modeling complex biological reactions. In that case, you might want to adjust your model to use the reaction rate evaluated at the old time level, a fully explicit approach. This is controlled by the variable theta, which can range from 0 to 1, where 0 is the full weighting of the rate at the old time level and 1 is fully weighting at the new time level. By default, X1t, X2t, and React are set to an use an average of the kinetic rates at the old and new time level with theta set at 0.6. To change to a fully explicit model, go to Config --> Stepping -> theta = 0. You can find more information regarding theta in 4.1 (Setting kinetic reactions) in the GWB Reaction Modeling Guide. 

If these suggestions didn't help with improving your run speed, please post your input file along with any custom databases so we can take a closer look. 

Hope this helps,
Jia Wang

Hi, Jia Wang:

GWB takes more than 99% of the CPU when I run X1t simulation (the attached figure). So I think CPU of our computer is out of date. This computer was bought in 2013. That is why I want to copy GWB to virtual machine or super computer in our university. Buying a new computer is also an option.

I will try your suggestions. But, can you tell me that if it is fesible/legal to copy GWB?

Huan

微信图片_20210130112201.jpg

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Hello Huan,

I hope that troubleshooting your script is going well. With regards to your other questions...

If you wish to use you machine for other tasks while X1t is performing the simulation, you can limit the number of threads available to X1t. By default, I believe the program is set to access all threads available on your CPU. To change this, go to the Config -> Stepping... and enter the number of threads you would like for X1t to have access to. 

It is possible to run GWB using a virtual machine but to have it save time on your run, it would need to have more CPU power than your current computer. 

To take full advantage of the capabilities of supercomputers with parallel processors would require special versions of X1t and X2t available in the GWB Advance Professional distribution. If you are interested in this, please refer to section 5 Cluster computing in the Reactive Transport Modeling User Guide for more information. 

Hope this helps,
Jia 

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