[AMBER] Amber20 CUDA.serial tests comparison failed with gb calculation: differences at e-01 level

From: 石谷沁 <guqin.shi.qilu-pharma.com>
Date: Fri, 7 May 2021 09:19:24 +0000

Hi All,

I’m back again after re-install the entire AMBER20/AMBERTools21.

My system is CentOS 7, CUDA kit is 11.1, GPU card is NVIDIA Quadro RTX5000 (*1)

I ran the “make test.cuda.serial”. Reports came back indicating 6 file comparisons failures.
===================================
243 file comparisons passed
6 file comparisons failed (1 of which can be ignored)
0 tests experienced errors
===================================

As David spotted last time, this is a genuine problem as the error is at level of e-01.
The errors are all about the Energy terms. EKtot are similar but EPtot are quite different giving the max. error shown below.

I noticed the differences all come from igb 7 & 8.
So at least for now, I’d better avoid CUDA calculation of MMGBSA with flag igb set to 7 & 8?
As David mentioned last time, I guess classic explicit solvent simulation is not affected, right?
===================================
possible FAILURE: check irest1_ntt0_igb7_ntc2.out.dif
/opt/amber20/test/cuda/gb_ala3
### Maximum absolute error in matching lines = 6.12e+00 at line 132 field 3
### Maximum relative error in matching lines = 4.05e-01 at line 168 field 3
---------------------------------------
possible FAILURE: check irest1_ntt0_igb8_ntc2.out.dif
/opt/amber20/test/cuda/gb_ala3
### Maximum absolute error in matching lines = 4.93e+00 at line 141 field 3
### Maximum relative error in matching lines = 3.07e-01 at line 177 field 3
---------------------------------------
possible FAILURE: check myoglobin_md_igb7.out.dif
/opt/amber20/test/cuda/myoglobin
### Maximum absolute error in matching lines = 7.80e+02 at line 62 field 3
### Maximum relative error in matching lines = 9.64e-01 at line 86 field 3
---------------------------------------
possible FAILURE: check myoglobin_md_igb8.out.dif
/opt/amber20/test/cuda/myoglobin
### Maximum absolute error in matching lines = 6.55e+02 at line 71 field 3
### Maximum relative error in matching lines = 6.51e-01 at line 201 field 4
---------------------------------------
possible FAILURE: check myoglobin_md_igb8_gbsa.out.dif
/opt/amber20/test/cuda/myoglobin
### Maximum absolute error in matching lines = 6.55e+02 at line 113 field 3
### Maximum relative error in matching lines = 9.67e-01 at line 154 field 2
---------------------------------------
possible FAILURE: (ignored) check myoglobin_md_igb8_gbsa3.out.dif
/opt/amber20/test/cuda/myoglobin
### Maximum absolute error in matching lines = 6.55e+02 at line 113 field 3
### Maximum relative error in matching lines = 7.22e-01 at line 152 field 4
===================================

By the way, I tried “make test.cuda.serial.SPFP”, but program told me there is no rule to follow:
make: *** No rule to make target 'test.cuda.serial.SPFP'. Stop.

So I can’t tell if the gbsa calculation comes from SPFP (default) or DPFP…anyway to sort this out?

Thank you a lot!
-Guqin



***********免责声明*************

本电子邮件中包含的信息仅供指定的或授权的个人或团体使用。本电子邮件及附件中提到的信息可能是保密信息或者法律特许保密的信息。如果你不是指定收件人,对于邮件内容的任何披露、复制、散布或者任何针对邮件内容进行的行为都是违法行为,需要严格禁止。如果您误收该电子邮件,请立即通知本公司并从您的系统中删除全部原始信息。该邮件可能会对您的系统或者数据造成损坏,对此我公司不承担任何责任。除非与公司业务有关,否则本邮件中的观点、结论、或者其它包含在邮件中的信息均为发件人个人行为,并不代表我公司。我公司有权保留对收发邮件的监控权利。

***********Business Email Disclaimer**************

 This e-mail and any attachments are meant for the intended recipient only and may contain information belonging to Qilu Pharma that is privileged, confidential, proprietary, and/or otherwise protected or prohibited from disclosure. If you are not the correct recipient or received this e-mail erroneously, please inform the sender immediately and delete this mail from your system. Qilu Pharma state no liability for any damage to your system and data caused by this email. Unless this email is related to the business with the company, otherwise any views or opinions presented in this email are solely from the sender. Qilu Pharma has the right to monitor the sending and receiving of the e-mail.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 07 2021 - 02:30:02 PDT
Custom Search