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load imbalance in GMX5+
- wanlingsong
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5 years 8 months ago #7769
by wanlingsong
load imbalance in GMX5+ was created by wanlingsong
Hi,
I am running a CG simulation using Martini 2 that contains multiple copies of a protein embedded in a membrane. I found that if I ran this simulation using GMX5+ and the mdp file provided by this website for GMX5, the load imbalance of the simualtion will gradually increase to over 80% from 4-10% at the beginning within a few hours. If I kill this the simulation job and restart it from where it stoped, the load imbalance will go back to 4-10% then again increase gradually.
However, if I ran the same simulation using GMX4.6, i.e. the exact same system configuration but with the mdp file provided by this website for GMX4, the load imbalance will remain stable at 4-10%.
I wondered if anyone has a similar issue and what gives rise to this.
Many thanks !
Wanling
I am running a CG simulation using Martini 2 that contains multiple copies of a protein embedded in a membrane. I found that if I ran this simulation using GMX5+ and the mdp file provided by this website for GMX5, the load imbalance of the simualtion will gradually increase to over 80% from 4-10% at the beginning within a few hours. If I kill this the simulation job and restart it from where it stoped, the load imbalance will go back to 4-10% then again increase gradually.
However, if I ran the same simulation using GMX4.6, i.e. the exact same system configuration but with the mdp file provided by this website for GMX4, the load imbalance will remain stable at 4-10%.
I wondered if anyone has a similar issue and what gives rise to this.
Many thanks !
Wanling
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- bart
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5 years 8 months ago #7779
by bart
Replied by bart on topic load imbalance in GMX5+
Hello Wanling,
I have a feeling this is a GMX5+ related issue, and does not have much to do with the Martin ff. So I would definetely also put the question on the Gromacs list if I where you. I also think we will need more information about the specifics you are doing to figure this one out.
I have a feeling this is a GMX5+ related issue, and does not have much to do with the Martin ff. So I would definetely also put the question on the Gromacs list if I where you. I also think we will need more information about the specifics you are doing to figure this one out.
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