GROMACS

Could you please provide the full cmake invocation as well. Based on the CMakeCache you provided everything should be working as expected:

GMX_CPU_ACCELERATION:STRING=SSE4.1
GMX_SUGGESTED_CPU_ACCELERATION:INTERNAL=SSE4.1

GNU_SSE4_CFLAG:INTERNAL=1
GNU_SSE4_CXXFLAG:INTERNAL=1
HAVE_SMMINTRIN_H:INTERNAL=1

I built using

ccmake ../release-4-6

The only variable settings I changed were related to FFTW since they were not auto-detected. I can try using cmake instead while manually specifying any necessary variables.

What cmake version is this?

Version 2.8.2 - do I need an upgrade? I suspect that's somewhat outdated.

That is old, but anything 2.8.x should in theory work. But the older ones are less tested.

I can reproduce it with cmake 2.8.2.

Roland Schulz wrote:

I can reproduce it with cmake 2.8.2.

That's weird, with cmake 2.8.0 it works for me. So what fails with 2.8.2? Justin's cache file suggests that both -msse4.1 and smmintrin.h checks have succeeded.

Never mind. I tested incorrectly. Can't reproduce it. Justin, did you delete CMakeCache.txt before you ran cmake? Do you get any warnings?

Roland Schulz wrote:

Never mind. I tested incorrectly. Can't reproduce it. Justin, did you delete CMakeCache.txt before you ran cmake? Do you get any warnings?

Almost everything I do fails, with one weird exception.

1. ccmake ../release-4-6 fails with the above
2. Removal of CMakeCache.txt and re-running ccmake ../release-4-6 does the exact same thing
3. The cmake command above (not ccmake) fails with the same thing
4. Running ccmake, removal of CMakeCache.txt, and then re-running cmake as shown above works. Why the heck is that the case?

Could you add line

message("Set: ${GROMACS_C_FLAGS_SET} Flags: ${GROMACS_C_FLAGS}")

Justin Lemkul wrote:

Roland Schulz wrote:

Never mind. I tested incorrectly. Can't reproduce it. Justin, did you delete CMakeCache.txt before you ran cmake? Do you get any warnings?

Almost everything I do fails, with one weird exception.

1. ccmake ../release-4-6 fails with the above
2. Removal of CMakeCache.txt and re-running ccmake ../release-4-6 does the exact same thing
3. The cmake command above (not ccmake) fails with the same thing

but this was without deleting CMakeCache.txt?

4. Running ccmake, removal of CMakeCache.txt, and then re-running cmake as shown above works. Why the heck is that the case?

We only set the flags the first time around. So if the first run of ccmake/cmake somehow messes up and then it doesn't help anymore to run cmake/ccmake again.
So it seems that cmake works but ccmake doesn't. What exactly did you do in ccmake?
1. Configure
2. change FFTW values
3. Configure

Or anything else?

Roland Schulz wrote:

Could you add line
[...]
before line 1070 (right after "NO MORE TESTS AFTER THIS LINE!")? And both the result of the message?

Result is:

Set:  Flags: -msse4.1 

Roland Schulz wrote:

Justin Lemkul wrote:

Roland Schulz wrote:

Never mind. I tested incorrectly. Can't reproduce it. Justin, did you delete CMakeCache.txt before you ran cmake? Do you get any warnings?

Almost everything I do fails, with one weird exception.

1. ccmake ../release-4-6 fails with the above
2. Removal of CMakeCache.txt and re-running ccmake ../release-4-6 does the exact same thing
3. The cmake command above (not ccmake) fails with the same thing

but this was without deleting CMakeCache.txt?

That's with an empty directory, starting over from scratch, just to test the difference between cmake and ccmake.

4. Running ccmake, removal of CMakeCache.txt, and then re-running cmake as shown above works. Why the heck is that the case?

We only set the flags the first time around. So if the first run of ccmake/cmake somehow messes up and then it doesn't help anymore to run cmake/ccmake again.
So it seems that cmake works but ccmake doesn't. What exactly did you do in ccmake?
1. Configure
2. change FFTW values
3. Configure

Or anything else?

That's it - the only problem is with finding FFTW.

I think I found the problem. It goes wrong if FFTW fails and thus the GROMACS_C_FLAGS aren't being written. Then the 2nd time around the flags aren't detected again. I'll verify. Just keeping this up to date, in case Szilard is looking at it too.