User 677b9c22ff
05-12-2009 23:23:59
Hi,
just came across this in jchem.version=5.2.4 WINXP as batch using cxcalc.
C:\XXX>cxcalc formula exactmass quak-quak-quak.smi
id Formula Exact mass
1 C18H28N2O4 340.233629858
2 C4H6N4O3S2 225.009673306
3 C34H47NO11 656.393898127
4 C22H24N2O2 350.198139254
5 C20H26N2O2 328.213789318
6 C17H13ClN4 308.082874143
7 C15H23NO2 251.187240217
8 C10H17N 151.136099549
9 C10H16N2O3S 247.109704926
10 C6H8ClN7O 230.055066236
11 C15H12ClN3O 286.074070344
12 C15H13N3O 252.113042669
13 C13H17N3O 232.144342797
The problem is the exactmass is not correct for these formulae.
MarvinView calculates them correctly, also JCHEM EXCEL.
NUM Formula OK ExactMass OK DIFF
1 C18H28N2O4 336.2049074 -4.028722464
2 C4H6N4O3S2 221.9881315 -3.021541848
3 C34H47NO11 645.3149114 -11.07898678
4 C22H24N2O2 348.183778 -2.014361232
5 C20H26N2O2 326.1994281 -2.014361232
6 C17H13ClN4 308.0828741 0
7 C15H23NO2 249.172879 -2.014361232
See attached file quak-quak-quak.smi.
Reminds me not only developers should always have testunits, but also
users should always use a validation set to monitor changes in algorithms etc.
For example if I run the same file several times I always get different results
Not sure if this is true for all the other parameters logp, logd, pka, wiener.
C:\XXX>cxcalc formula exactmass quak-quak-quak.smi
id Formula Exact mass
1 C18H28N2O4 340.233629858
2 C4H6N4O3S2 225.009673306
3 C34H47NO11 656.393898127
4 C22H24N2O2 350.198139254
5 C20H26N2O2 328.213789318
6 C17H13ClN4 308.082874143
7 C15H23NO2 251.187240217
8 C10H17N 151.136099549
9 C10H16N2O3S 247.109704926
10 C6H8ClN7O 230.055066236
11 C15H12ClN3O 286.074070344
12 C15H13N3O 252.113042669
13 C13H17N3O 232.144342797
C:\XXX>cxcalc formula exactmass quak-quak-quak.smi
id Formula Exact mass
1 C18H28N2O4 336.204907394
2 C4H6N4O3S2 221.988131458
3 C34H47NO11 645.314911351
4 C22H24N2O2 348.183778022
5 C20H26N2O2 326.199428086
6 C17H13ClN4 308.082874143
7 C15H23NO2 249.172878985
8 C10H17N 151.136099549
9 C10H16N2O3S 244.088163078
10 C6H8ClN7O 229.047885620
11 C15H12ClN3O 285.066889728
12 C15H13N3O 251.105862053
13 C13H17N3O 231.137162181
C:\XXX>
I am pretty sure that is a serious bug, because also with other files
the same happens.I just dont know how and why this could happen.
Tobias
ChemAxon e08c317633
07-12-2009 22:03:11
Hi Tobias,
It seems to be a concurrency issue (cxcalc utilizes all CPU cores for the calculation). Please use the "-s" cxcalc switch (undocumented) until we fix this error. It will run the calculations in single mode (on one CPU core).
Example:
$ cxcalc -s formula exactmass quak-quak-quak.smi
id Formula Exact mass
1 C18H28N2O4 336,204907394
2 C4H6N4O3S2 221,988131458
3 C34H47NO11 645,314911351
4 C22H24N2O2 348,183778022
5 C20H26N2O2 326,199428086
6 C17H13ClN4 308,082874143
7 C15H23NO2 249,172878985
8 C10H17N 151,136099549
9 C10H16N2O3S 244,088163078
10 C6H8ClN7O 229,047885620
11 C15H12ClN3O 285,066889728
12 C15H13N3O 251,105862053
13 C13H17N3O 231,137162181
Only cxcalc runs the ElementalAnalyserPlugin calculations concurrently, that's why MarvinSketch/View and JChem for Excel return the correct results.
We tried to reproduce this error with other calculations (pKa, logP, PSA, etc.) using Marvin 5.2.4, but these seems to work fine. Also, with Marvin 5.3 (will be released soon) this exactmass bug is not reproducible.
We will get back to you when we find out more about this bug.
Zsolt
User 677b9c22ff
07-12-2009 23:32:24
Hi Zsolt,
oohhh the wonders of concurrency. Thanks for the upcoming fix, its pretty clear though that 4,8,12,16, 80 cores will be the future, so dealing with software threading issues at an early stage is clearly an advantage. How hard is it to convince people that instead of waiting one hour they only have to wait 2 minutes when using a 32 thread SMP setup. :-)
Allthough I have to say the -s switch does not do anything for exactmass in the older 5.2.2 version, its neither faster nor slower and using the same number of threads (dont know how well they are utilized).
However in case of logP which seems to be better parallelized it does soemthing, CPU use is lower with -s and also the thread count drops from 12 to 10.
I also tried to reproduce with the older version 5.2.2 but that version seems fine, could be also a JAVA version issue.
Cheers
Tobias
User 677b9c22ff
04-01-2010 16:24:24
Hi,
I just came across another weird behaviour, after using the safe switch (single threaded) cxcalc -s for around 10 times, cxcalc was spitting out integer values, when the -s switch was not used anymore.
C:\temp>cxcalc -s formula exactmass quak-quak-quak.smi
id Formula Exact mass
1 C18H28N2O4 336.204907394
2 C4H6N4O3S2 221.988131458
3 C34H47NO11 645.314911351
4 C22H24N2O2 348.183778022
5 C20H26N2O2 326.199428086
6 C17H13ClN4 308.082874143
7 C15H23NO2 249.172878985
8 C10H17N 151.136099549
9 C10H16N2O3S 244.088163078
10 C6H8ClN7O 229.047885620
11 C15H12ClN3O 285.066889728
12 C15H13N3O 251.105862053
13 C13H17N3O 231.137162181
C:\temp>cxcalc formula exactmass quak-quak-quak.smi
id Formula Exact mass
1 C18H28N2O4 308
2 C4H6N4O3S2 216
3 C34H47NO11 598
4 C22H24N2O2 324
5 C20H26N2O2 300
6 C17H13ClN4 295
7 C15H23NO2 226
8 C10H17N 134
9 C10H16N2O3S 228
10 C6H8ClN7O 221
11 C15H12ClN3O 273
12 C15H13N3O 238
13 C13H17N3O 214
This is still the old version (jchem.vernum=5.2.4, WINXP32) just to make sure that the commandline use is ok in the next release because I think its quite powerful and I use it quite often.
Thanks
Tobias
User 677b9c22ff
04-01-2010 16:34:29
Hi,
I just came across another weird behaviour, after using the safe switch (single threaded) cxcalc -s for around 10 times, cxcalc was spitting out integer values, when the -s switch was not used anymore.
C:\temp>cxcalc -s formula exactmass quak-quak-quak.smi
id Formula Exact mass
1 C18H28N2O4 336.204907394
2 C4H6N4O3S2 221.988131458
3 C34H47NO11 645.314911351
4 C22H24N2O2 348.183778022
5 C20H26N2O2 326.199428086
6 C17H13ClN4 308.082874143
7 C15H23NO2 249.172878985
8 C10H17N 151.136099549
9 C10H16N2O3S 244.088163078
10 C6H8ClN7O 229.047885620
11 C15H12ClN3O 285.066889728
12 C15H13N3O 251.105862053
13 C13H17N3O 231.137162181
C:\temp>cxcalc formula exactmass quak-quak-quak.smi
id Formula Exact mass
1 C18H28N2O4 308
2 C4H6N4O3S2 216
3 C34H47NO11 598
4 C22H24N2O2 324
5 C20H26N2O2 300
6 C17H13ClN4 295
7 C15H23NO2 226
8 C10H17N 134
9 C10H16N2O3S 228
10 C6H8ClN7O 221
11 C15H12ClN3O 273
12 C15H13N3O 238
13 C13H17N3O 214
This is still the old version (jchem.vernum=5.2.4, WINXP32) just to make sure that the commandline use is ok in the next release because I think its quite powerful and I use it quite often.
java version "1.6.0_11"
Java(TM) SE Runtime Environment (build 1.6.0_11-b03)
Java HotSpot(TM) Client VM (build 11.0-b16, mixed mode, sharing)
In case of the JAVA server version, there is also sometimes a digit cut off (see 2nd) and the values are false. With -server -s there seems to be no problem
C:\temp>cxcalc -server formula exactmass quak-quak-quak.smi
id Formula Exact mass
1 C18H28N2O4 336.204907394
2 C4H6N4O3S2 222.174
3 C34H47NO11 645.314911351
4 C22H24N2O2 348.183778022
5 C20H26N2O2 326.199428086
6 C17H13ClN4 308.082874143
7 C15H23NO2 249.172878985
8 C10H17N 151.136099549
9 C10H16N2O3S 244.088163078
10 C6H8ClN7O 229.047885620
11 C15H12ClN3O 285.066889728
12 C15H13N3O 251.105862053
13 C13H17N3O 231.137162181
Thanks
Tobias
ChemAxon e08c317633
07-01-2010 15:05:18
Hi Tobias,
Thanks for further information.
To fix this error we will internally disabled concurrent execution of ElementalAnalyserPlugin calculations in Marvin 5.2.7 (next Marvin patch release). ElementalAnalyser calculations are fast, so speed decrease should not be relevant. In Marvin 5.2.0 - 5.2.6 versions the "-s" cxcalc switch workaround should be used, as described in previous posts.
Marvin 5.3 (coming) is not affected by this bug, so in that version concurrent execution will be enabled.
Zsolt