Finished tests:
Finished test suite for AmberTools
2418 file comparisons passed
19 file comparisons failed ( 1 ignored)
5 tests experienced errors
I'll go through the logs and see what these issues might be. Meanwhile, the MPI compilation worked with openMPI (latest version from brew) though I still cannot run the tests without my firewall going insane with popups so I don't know if this finishes without hidden problems.
As for trying to compile using only the GNU compilers:
./configure gnu
Checking NetCDF...
Using bundled NetCDF library.
Starting NetCDF build.
Configuring NetCDF C interface (may be time-consuming)...
Compiling the NetCDF C interface (may be time-consuming)...
Error: NetCDF C compile failed.
Check /amber18/AmberTools/src/netcdf-4.6.1/netcdf.c.compile.log
for errors.
Configure failed due to the errors above!
-->
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/resource.h:443:29: error: parameter name omitted
443 | int getiopolicy_np(int, int) __OSX_AVAILABLE_STARTING(__MAC_10_5, __IPHONE_2_0);
| ^~~
dparallel.c:394: error: expected '{' at end of input
394 | }
|
make[1]: *** [libdispatch_la-dparallel.lo] Error 1
make: *** [install-recursive] Error 1
I still see a lot of references to CLT in this log file even though I've set all needed compilers to the GNU versions, I suppose this might be fixed by also installing the external NetCDF libraries from brew and pointing to these during config.
Best regards
// Gustaf
________________________________
Från: Tru Huynh <tru.pasteur.fr>
Skickat: den 17 oktober 2019 17:36:36
Till: AMBER Mailing List
Ämne: Re: [AMBER] (long) OSX/catalina Ambertools19 building success with brew
Hi,
Glad it helped,
On Wed, Oct 16, 2019 at 08:46:00PM +0000, Gustaf Olsson wrote:
> Thank you very much, identical setup regarding macOS, GCC/GFORTRAN and Xcode
>
>
...
>
> Workaround/solution confimed. No tests run yet and still amber18 as well as MPI/openMPI versions needs to be confirmed.
>
with 10.14 or 10.15 and clang only (make clean ; ./configure clang && make install && make test)
Finished test suite for AmberTools at Tue Oct 15 22:13:35 CEST 2019.
2436 file comparisons passed
1 file comparisons failed ( 1 ignored)
5 tests experienced errors
Test log file saved as /Users/tru/ambertools19/amber18/logs/test_at_serial/2019-10-15_20-26-15.log
Test diffs file saved as /Users/tru/ambertools19/amber18/logs/test_at_serial/2019-10-15_20-26-15.diff
which contains
possible FAILURE: (ignored) check FINAL_RESULTS_MMPBSA_1.dat.dif
/Users/tru/ambertools19/amber18/AmberTools/test/mmpbsa_py/07_Comprehensive
39c39
< Total -13.7036 1.8048 0.8071
> Total -7.4211 2.0042 0.8963
108c108
< Using Normal Mode Entropy Approximation: DELTA G binding = 6.4576 +/- 8.7090
> Using Normal Mode Entropy Approximation: DELTA G binding = 0.3641 +/- 8.7599
181c181
< Using Normal Mode Entropy Approximation: DELTA G binding = 7.8758 +/- 8.2601
> Using Normal Mode Entropy Approximation: DELTA G binding = 1.5912 +/- 8.3060
### Maximum absolute error in matching lines = 6.28e+00 at line 181 field 10
### Maximum relative error in matching lines = 1.67e+01 at line 108 field 10
---------------------------------------
the ignored was caused by:
==============================================================
cd ccif && ./Run.ccif
./Run.ccif: Program error
make[3]: [test] Error 1 (ignored)
cd charge_equlibration && ./Run.equ_charge
Step1: run antechamber to generate resp charges with '-eq 0'
Step2: run antechamber to generate resp charges with '-eq 1'
Step3: run antechamber to generate resp charges with '-eq 2'
Step4: run antechamber to generate bcc charges with '-eq 0'
Step5: run antechamber to generate bcc charges with '-eq 1'
Step6: run antechamber to generate bcc charges with '-eq 2'
diffing c4h4cl2_eq0.mol2.save with c4h4cl2_eq0.mol2
PASSED
with 10.14 and 10.15 with "./configure -macAccelerate clang"
Finished test suite for AmberTools at Wed Oct 16 10:34:42 CEST 2019.
2435 file comparisons passed
2 file comparisons failed ( 2 ignored)
5 tests experienced errors
Test log file saved as /Users/tru/ambertools19/amber18/logs/test_at_serial/2019-10-16_08-52-57.log
Test diffs file saved as /Users/tru/ambertools19/amber18/logs/test_at_serial/2019-10-16_08-52-57.diff
make[1]: *** [test] Error 1
make: [test.serial] Error 2 (ignored)
which contains:
possible FAILURE: (ignored) check FINAL_RESULTS_MMPBSA_1.dat.dif
/Users/tru/ambertools19/amber18/AmberTools/test/mmpbsa_py/07_Comprehensive
39c39
< Total -13.7036 1.8048 0.8071
> Total -7.4211 2.0042 0.8963
108c108
< Using Normal Mode Entropy Approximation: DELTA G binding = 6.4576 +/- 8.7090
> Using Normal Mode Entropy Approximation: DELTA G binding = 0.3641 +/- 8.7599
181c181
< Using Normal Mode Entropy Approximation: DELTA G binding = 7.8758 +/- 8.2601
> Using Normal Mode Entropy Approximation: DELTA G binding = 1.5912 +/- 8.3060
### Maximum absolute error in matching lines = 6.28e+00 at line 181 field 10
### Maximum relative error in matching lines = 1.67e+01 at line 108 field 10
---------------------------------------
possible FAILURE: (ignored) check min.out.dif
/Users/tru/ambertools19/amber18/test/sebomd/AM1-d-CB1/dimethylether
105c105
< 5 -4.6175E+1 3.4117 6.4413 H12 4
> 5 -4.6175E+1 3.4117 6.4413 H13 5
---------------------------------------
==============================================================
cd mmpbsa_py && /Library/Developer/CommandLineTools/usr/bin/make test
cd 07_Comprehensive && ./Run.comprehensive
diffing FINAL_RESULTS_MMPBSA_1.dat.save with FINAL_RESULTS_MMPBSA_1.dat
possible FAILURE: (ignored) check FINAL_RESULTS_MMPBSA_1.dat.dif
==============================================================
cd sebomd/AM1-d-CB1/dimethylether && ./min.csh && ./md.csh
diffing min.out.save with min.out
possible FAILURE: (ignored) check min.out.dif
==============================================================
In all cases I get a FPE error for:
cd dhfr && ./Run.dhfr.min_prcg
Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Backtrace for this error:
#0 0x11947af5d
#1 0x11947a36d
#2 0x7fff7230cb1c
#3 0x101cf490f
#4 0x101d5ddfa
#5 0x101d54e0c
#6 0x101d54e6b
Floating exception
./Run.dhfr.min_prcg: Program error
make[2]: [test.sander.BASIC] Error 1 (ignored)
cd dhfr && ./Run.dhfr.xmin
Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Backtrace for this error:
#0 0x11dd0af5d
#1 0x11dd0a36d
#2 0x7fff7230cb1c
#3 0x10658390f
#4 0x1065ecdfa
#5 0x1065e3e0c
#6 0x1065e3e6b
Floating exception
./Run.dhfr.xmin: Program error
make[2]: [test.sander.BASIC] Error 1 (ignored)
cd ff14ipq && ./Run.ff14ipq
diffing mdout.ff14ipq.save with mdout.ff14ipq
PASSED
and
cd rism3d/ala && ./Run.ala.min
Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Backtrace for this error:
#0 0x11d6c5f5d
#1 0x11d6c536d
#2 0x7fff7230cb1c
#3 0x105f3f90f
#4 0x105fa8dfa
#5 0x105f9fe0c
#6 0x105f9fe6b
Floating exception
./Run.ala.min: Program error
make[2]: [test.sander.RISM] Error 1 (ignored)
cd rism3d/ala && ./Run.ala.imin5
diffing ala.imin5.out.save.totChg with ala.imin5.out.totChg
PASSED
Cheers
Tru
--
Tru Huynh (PhD) | mailto:tru.pasteur.fr | tel +33 1 45 68 87 37
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France
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Received on Thu Oct 17 2019 - 12:30:02 PDT
