Hi
I am working on porting Fedora distribution to AArch64 (64-bit ARM)
architecture. One of our main blockers now is openbabel.
Package builds fine but then there are 3 test failures:
The following tests FAILED:
10 - rotor_Test (Failed)
23 - inchiSteffen_PubChem.smi_Test (Timeout)
54 - pytest_sym (Timeout)
I looked at rotor one and filled bug for your project:
https://sourceforge.net/p/openbabel/bugs/927/
But as there was no answer I decided to do some more digging and post to
this mailing list.
Attached patch adds printing of rotor::CalcTorsion variables so I can
see how it goes during test. rotor-aarch64.txt is log output on AArch64
platform and rotor-x86_64.txt is the same code but run on x86-64.
As you see there are differences between results and currently I lack
ideas why.
Index: openbabel-2.3.2/src/rotor.cpp
===================================================================
--- openbabel-2.3.2.orig/src/rotor.cpp
+++ openbabel-2.3.2/src/rotor.cpp
@@ -22,6 +22,8 @@ GNU General Public License for more deta
#include <openbabel/mol.h>
#include <openbabel/rotor.h>
+#include <iostream>
+
// private data headers with default parameters
#include "torlib.h"
@@ -643,6 +645,33 @@ namespace OpenBabel
if (costheta > 0.9999999)
costheta = 0.9999999;
+ std::cout << "-------------------------------------" << std::endl;
+ std::cout << "v1x = " << v1x << std::endl;
+ std::cout << "v1y = " << v1y << std::endl;
+ std::cout << "v1z = " << v1z << std::endl;
+ std::cout << "v2x = " << v2x << std::endl;
+ std::cout << "v2y = " << v2y << std::endl;
+ std::cout << "v2z = " << v2z << std::endl;
+ std::cout << "v3x = " << v3x << std::endl;
+ std::cout << "v3y = " << v3y << std::endl;
+ std::cout << "v3z = " << v3z << std::endl;
+ std::cout << std::endl;
+ std::cout << "c1x = " << c1x << std::endl;
+ std::cout << "c1y = " << c1y << std::endl;
+ std::cout << "c1z = " << c1z << std::endl;
+ std::cout << "c2x = " << c2x << std::endl;
+ std::cout << "c2y = " << c2y << std::endl;
+ std::cout << "c2z = " << c2z << std::endl;
+ std::cout << "c3x = " << c3x << std::endl;
+ std::cout << "c3y = " << c3y << std::endl;
+ std::cout << "c3z = " << c3z << std::endl;
+
+ std::cout << "v2x*c3x = " << v2x*c3x << std::endl;
+ std::cout << "v2y*c3y = " << v2y*c3y << std::endl;
+ std::cout << "v2z*c3z = " << v2z*c3z << std::endl;
+
+ std::cout << "(v2x*c3x + v2y*c3y + v2z*c3z) = " << (v2x*c3x + v2y*c3y + v2z*c3z) << std::endl;
+
if ((v2x*c3x + v2y*c3y + v2z*c3z) > 0.0)
ang = -acos(costheta);
else
UpdateCTestConfiguration from
:/builddir/build/BUILD/openbabel-2.3.2/DartConfiguration.tcl
Parse Config file:/builddir/build/BUILD/openbabel-2.3.2/DartConfiguration.tcl
UpdateCTestConfiguration from
:/builddir/build/BUILD/openbabel-2.3.2/DartConfiguration.tcl
Parse Config file:/builddir/build/BUILD/openbabel-2.3.2/DartConfiguration.tcl
Test project /builddir/build/BUILD/openbabel-2.3.2
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: rotor_Test
1: Test command: /builddir/build/BUILD/openbabel-2.3.2/bin/test_rotor
1: Test timeout computed to be: 1500
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = -1.31002
1: v3y = -0.796717
1: v3z = -0.034438
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 0.00209203
1: c2y = -0.0982675
1: c2z = 2.19382
1: c3x = -2.66578e-06
1: c3y = 2.05612e-06
1: c3z = 9.46416e-08
1: v2x*c3x = 3.23619e-06
1: v2y*c3y = 1.92523e-06
1: v2z*c3z = 4.07896e-09
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 5.1655e-06
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = -1.31002
1: v3y = -0.796717
1: v3z = -0.034438
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 0.00209203
1: c2y = -0.0982675
1: c2z = 2.19382
1: c3x = -2.66578e-06
1: c3y = 2.05612e-06
1: c3z = 9.46416e-08
1: v2x*c3x = 3.23619e-06
1: v2y*c3y = 1.92523e-06
1: v2z*c3z = 4.07896e-09
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 5.1655e-06
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = 0.0040695
1: v3y = 0.846568
1: v3z = 1.27883
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 1.16093
1: c2y = 1.55264
1: c2z = -1.03152
1: c3x = 3.30486
1: c3y = -2.54904
1: c3z = -0.11733
1: v2x*c3x = -4.01201
1: v2y*c3y = -2.38677
1: v2z*c3z = -0.00505682
1: (v2x*c3x + v2y*c3y + v2z*c3z) = -6.40384
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = -1.31002
1: v3y = -0.796717
1: v3z = -0.034438
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 0.00209203
1: c2y = -0.0982675
1: c2z = 2.19382
1: c3x = -2.66578e-06
1: c3y = 2.05612e-06
1: c3z = 9.46416e-08
1: v2x*c3x = 3.23619e-06
1: v2y*c3y = 1.92523e-06
1: v2z*c3z = 4.07896e-09
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 5.1655e-06
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = -1.31002
1: v3y = -0.796717
1: v3z = -0.034438
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 0.00209203
1: c2y = -0.0982675
1: c2z = 2.19382
1: c3x = -2.66578e-06
1: c3y = 2.05612e-06
1: c3z = 9.46416e-08
1: v2x*c3x = 3.23619e-06
1: v2y*c3y = 1.92523e-06
1: v2z*c3z = 4.07896e-09
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 5.1655e-06
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = 0.0040695
1: v3y = 0.846568
1: v3z = 1.27883
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 1.16093
1: c2y = 1.55264
1: c2z = -1.03152
1: c3x = 3.30486
1: c3y = -2.54904
1: c3z = -0.11733
1: v2x*c3x = -4.01201
1: v2y*c3y = -2.38677
1: v2z*c3z = -0.00505682
1: (v2x*c3x + v2y*c3y + v2z*c3z) = -6.40384
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = 0.440074
1: v3y = 1.46771
1: v3z = 0.0653222
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = -0.00209297
1: c2y = 0.0982663
1: c2z = -2.19382
1: c3x = -1.18684e-16
1: c3y = 1.0024e-16
1: c3z = 4.61789e-18
1: v2x*c3x = 1.4408e-16
1: v2y*c3y = 9.38587e-17
1: v2z*c3z = 1.99026e-19
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 2.38138e-16
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = 0.440074
1: v3y = 1.46771
1: v3z = 0.0653222
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = -0.00209297
1: c2y = 0.0982663
1: c2z = -2.19382
1: c3x = -1.18684e-16
1: c3y = 1.0024e-16
1: c3z = 4.61789e-18
1: v2x*c3x = 1.4408e-16
1: v2y*c3y = 9.38587e-17
1: v2z*c3z = 1.99026e-19
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 2.38138e-16
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = -1.31002
1: v3y = -0.796694
1: v3z = -0.0349442
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 0.00161712
1: c2y = -0.098882
1: c2z = 2.19379
1: c3x = -0.00135339
1: c3y = 0.00104387
1: c3z = 4.80486e-05
1: v2x*c3x = 0.00164298
1: v2y*c3y = 0.00097742
1: v2z*c3z = 2.07085e-06
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 0.00262247
1: /builddir/build/BUILD/openbabel-2.3.2/test/rotortest.cpp:123:
IsNear(RAD_TO_DEG * rotor.CalcTorsion(mol->GetCoordinates()), 180.0, 1.0) (FAIL)
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = 0.440074
1: v3y = 1.46768
1: v3z = 0.0659619
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = -0.00149277
1: c2y = 0.0990429
1: c2z = -2.19379
1: c3x = 0.00170706
1: c3y = -0.00131666
1: c3z = -6.06047e-05
1: v2x*c3x = -0.00207233
1: v2y*c3y = -0.00123284
1: v2z*c3z = -2.612e-06
1: (v2x*c3x + v2y*c3y + v2z*c3z) = -0.00330778
1/1 Test #1: rotor_Test .......................***Failed Error regular
expression found in output. Regex=[FAIL] 0.16 sec
0% tests passed, 1 tests failed out of 1
Total Test time (real) = 0.17 sec
The following tests FAILED:
1 - rotor_Test (Failed)
UpdateCTestConfiguration from
:/builddir/build/BUILD/openbabel-2.3.2/DartConfiguration.tcl
Parse Config file:/builddir/build/BUILD/openbabel-2.3.2/DartConfiguration.tcl
UpdateCTestConfiguration from
:/builddir/build/BUILD/openbabel-2.3.2/DartConfiguration.tcl
Parse Config file:/builddir/build/BUILD/openbabel-2.3.2/DartConfiguration.tcl
Test project /builddir/build/BUILD/openbabel-2.3.2
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: rotor_Test
1: Test command: /builddir/build/BUILD/openbabel-2.3.2/bin/test_rotor
1: Test timeout computed to be: 1500
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = -1.31002
1: v3y = -0.796717
1: v3z = -0.034438
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 0.00209203
1: c2y = -0.0982675
1: c2z = 2.19382
1: c3x = -2.66578e-06
1: c3y = 2.05612e-06
1: c3z = 9.46416e-08
1: v2x*c3x = 3.23619e-06
1: v2y*c3y = 1.92523e-06
1: v2z*c3z = 4.07896e-09
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 5.1655e-06
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = -1.31002
1: v3y = -0.796717
1: v3z = -0.034438
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 0.00209203
1: c2y = -0.0982675
1: c2z = 2.19382
1: c3x = -2.66578e-06
1: c3y = 2.05612e-06
1: c3z = 9.46416e-08
1: v2x*c3x = 3.23619e-06
1: v2y*c3y = 1.92523e-06
1: v2z*c3z = 4.07896e-09
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 5.1655e-06
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = 0.0040695
1: v3y = 0.846568
1: v3z = 1.27883
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 1.16093
1: c2y = 1.55264
1: c2z = -1.03152
1: c3x = 3.30486
1: c3y = -2.54904
1: c3z = -0.11733
1: v2x*c3x = -4.01201
1: v2y*c3y = -2.38677
1: v2z*c3z = -0.00505682
1: (v2x*c3x + v2y*c3y + v2z*c3z) = -6.40384
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = -1.31002
1: v3y = -0.796717
1: v3z = -0.034438
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 0.00209203
1: c2y = -0.0982675
1: c2z = 2.19382
1: c3x = -2.66578e-06
1: c3y = 2.05612e-06
1: c3z = 9.46416e-08
1: v2x*c3x = 3.23619e-06
1: v2y*c3y = 1.92523e-06
1: v2z*c3z = 4.07896e-09
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 5.1655e-06
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = -1.31002
1: v3y = -0.796717
1: v3z = -0.034438
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 0.00209203
1: c2y = -0.0982675
1: c2z = 2.19382
1: c3x = -2.66578e-06
1: c3y = 2.05612e-06
1: c3z = 9.46416e-08
1: v2x*c3x = 3.23619e-06
1: v2y*c3y = 1.92523e-06
1: v2z*c3z = 4.07896e-09
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 5.1655e-06
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = 0.0040695
1: v3y = 0.846568
1: v3z = 1.27883
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 1.16093
1: c2y = 1.55264
1: c2z = -1.03152
1: c3x = 3.30486
1: c3y = -2.54904
1: c3z = -0.11733
1: v2x*c3x = -4.01201
1: v2y*c3y = -2.38677
1: v2z*c3z = -0.00505682
1: (v2x*c3x + v2y*c3y + v2z*c3z) = -6.40384
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = 0.440074
1: v3y = 1.46771
1: v3z = 0.0653222
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = -0.00209297
1: c2y = 0.0982663
1: c2z = -2.19382
1: c3x = 6.66134e-16
1: c3y = -4.70977e-16
1: c3z = -2.17654e-17
1: v2x*c3x = -8.0867e-16
1: v2y*c3y = -4.40995e-16
1: v2z*c3z = -9.38065e-19
1: (v2x*c3x + v2y*c3y + v2z*c3z) = -1.2506e-15
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = 0.440074
1: v3y = 1.46771
1: v3z = 0.0653222
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = -0.00209297
1: c2y = 0.0982663
1: c2z = -2.19382
1: c3x = 6.66134e-16
1: c3y = -4.70977e-16
1: c3z = -2.17654e-17
1: v2x*c3x = -8.0867e-16
1: v2y*c3y = -4.40995e-16
1: v2z*c3z = -9.38065e-19
1: (v2x*c3x + v2y*c3y + v2z*c3z) = -1.2506e-15
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = -1.31002
1: v3y = -0.796751
1: v3z = -0.0336648
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = 0.00281751
1: c2y = -0.0973288
1: c2z = 2.19386
1: c3x = 0.00206073
1: c3y = -0.00158944
1: c3z = -7.31608e-05
1: v2x*c3x = -0.00250167
1: v2y*c3y = -0.00148826
1: v2z*c3z = -3.15316e-06
1: (v2x*c3x + v2y*c3y + v2z*c3z) = -0.00399308
1: -------------------------------------
1: v1x = -1.31002
1: v1y = -0.796717
1: v1z = -0.034437
1: v2x = -1.21398
1: v2y = 0.93634
1: v2z = 0.043099
1: v3x = 0.440073
1: v3y = 1.46774
1: v3z = 0.0646825
1:
1: c1x = -0.00209297
1: c1y = 0.0982663
1: c1z = -2.19382
1: c2x = -0.00269317
1: c2y = 0.0974897
1: c2z = -2.19385
1: c3x = -0.00170706
1: c3y = 0.00131666
1: c3z = 6.06047e-05
1: v2x*c3x = 0.00207233
1: v2y*c3y = 0.00123284
1: v2z*c3z = 2.612e-06
1: (v2x*c3x + v2y*c3y + v2z*c3z) = 0.00330778
1/1 Test #1: rotor_Test ....................... Passed 0.06 sec
100% tests passed, 0 tests failed out of 1
Total Test time (real) = 0.06 sec
------------------------------------------------------------------------------
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