<div dir="ltr"><div class="gmail_extra"><div><br></div><div class="gmail_quote">On Fri, Feb 8, 2013 at 5:34 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><br><br><div class="gmail_quote"><div class="im">On Tue, Feb 5, 2013 at 8:58 PM, Szilárd Páll <span dir="ltr"><<a href="mailto:szilard.pall@cbr.su.se" target="_blank">szilard.pall@cbr.su.se</a>></span> wrote:<br>
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<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div><br></div><div>Note that I'm not talking about some magic override, but simply the ability to go to the flags and remove e.g. the "-ip" icc flag which I know that it can in some cases cause performance regression.<br>
</div></div></div></div></blockquote></div><div><br>In a fresh release-4-6 build tree, if you use</div><div><br></div><div>CC=icc cmake .. -DGMXC_CFLAGS_RELEASE="-no-ip"</div><div><br></div><div>you get</div><div>
<br>
</div><div>cd /nethome/mark/git/another-r46/build-cmake-amd2/src/gmxlib && /opt/intel/composer_xe_2011_sp1.9.293/bin/intel64/icc -Dgmx_EXPORTS -DTMPI_SET_AFFINITY -DHAVE_CONFIG_H -DHAVE_RDTSCP -DTMPI_EXPORTS -msse2 -std=gnu99 -Wall -ip -funroll-all-loops -no-ip -O3 -DNDEBUG -fPIC -I/nethome/mark/git/another-r46/build-cmake-amd2/src -I/nethome/mark/git/another-r46/build-cmake-amd2/include -I/nethome/mark/git/another-r46/include -I/nethome/mark/git/another-r46/src/gmxlib -openmp -o CMakeFiles/gmx.dir/rmpbc.c.o -c /nethome/mark/git/another-r46/src/gmxlib/rmpbc.c</div>
<div><br></div><div>which seems to do roughly what you want, from a one-shot, because we have partially segmented the sets of flags GROMACS adds, and prepend them for each run of cmake. In this case, GMXC_CFLAGS_RELEASE is the magic name for the C flags we add for the Release build type. Because we prepend the flags to the initial value (which is initially unset by GROMACS), the value passed in from the command line is there at the end. Then, because GROMACS no longer caches the flags we generate, things can be changed later.</div>
</div></blockquote><div><br></div><div style>Thanks, that indeed seems to be a decent workaround for my very specific example. Unfortunately, this won't work in general. It will only work if the user wants to remove/inactivate a GROMACS-default compiler flag which happens to have a -no-FOO pair.</div>
<div style><br></div><div style>It would be good to document this, but as it only works in a corner case I'm not sure it's worth it.<br></div><div style> <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
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<div><br></div><div>Note that CMake caches that command-line initial value itself, so that the next call to cmake will also result in -no-ip. Then when you want some other set of flags, without touching the cache you can do</div>
<div><br></div><div>CC=icc cmake .. -DGMXC_CFLAGS_RELEASE=""</div><div><br></div><div>and this reverts to the out-of-the-box functionality (or you could try a new set of flags if you wanted).</div><div><br></div>
<div>Your original example where -m and -x conflict and lead to warnings is irritating, but not a deal-breaker. Using GMX_SKIP_DEFAULT_CFLAGS provides a two-step approach to fixing that. Obviously, make knows how to tell the compiler the right things to do (e.g. src/buildinfo.h has the full CFLAGS in it), so a *make* target that printed out the CFLAGS (whole and/or in parts) might be a useful thing.</div>
</div></blockquote><div><br></div><div style>Sure, that's all clear to me, except that the "two step approach" requires more like 4 steps :) Additionally it is really easy to screw up for the aforementioned reasons (see the details on the risk of unknowingly removing -O3).</div>
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<div><br></div><div>There's currently no way to say "cmake -DUSE_MY_FLAGS_ONLY_IM_SUPER_SMART=-blahblah". I'm not philosophically opposed to having one, but since compilers normally act on the last of a series of inconsistent flags, the above approaches seem workable if we document them in an advanced section of the installation guide. I think there are probably more not-competent-enough users who'd wrongly try to use it (or use it wrongly) and run into problems than smart-enough users/admins with a real need case.</div>
</div></blockquote><div><br></div><div style>That's exactly why I'm not certain that this workaround is worth documenting. The problem is that the above approach solves only a special case: </div><div style>- will only work for removing a -FOO for which there is a "-no-FOO" *and*</div>
<div style>- the compiler used has the policy of silently overriding flags.</div><div style><br></div><div style>Not only that there is no way to set a "USE_MY_FLAGS_ONLY_IM_SUPER_SMART" variable, but the GMX_SKIP_DEFAULT_CFLAGS workflow is IMO too complicated and fragile (ref:-O3 issue) even for advanced users.</div>
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<div><br></div><div><div>Is there anything you want to be able to do that these kinds of workflows do not support?</div></div></div></blockquote><div><br></div><div style>Uhmm, I guess I should clarify this. I am not trying to solve some burning issue that has suddenly crippled me. All my examples were simply use-cases meant to illustrate real-world scenarios in which the new behavior of the build system causes issues. </div>
<div style><br></div><div style>So let me state it again: I am trying to discuss usability concerns of our build system that affect the type B users (i.e people familiar with the concept of compiler flags, comipler optimization, CFLAGS, etc).</div>
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<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>In my eyes, reviewing and changing flags is much more important than the consistency of acceleration flags across cmake reruns, that's why I find it unfortunate that the build system got crippled in an attempt to fix that issue. Of course, I am biased, but putting aside the fact that I will suffer from this build system "behaviour regression", I think many sysadmins and other advanced users will also be scratching their heads.<br>
</div></div></div></div></blockquote><div><br></div></div><div>If so, gmx-users must have some filters on it ;-)</div></div></blockquote><div><br></div><div style>I hope you are not suggesting that:</div><div style>"not (exists complaints) => not (exists issues)"</div>
<div style><br></div><div style>GROMACS 4.6 has been out for just a few weeks and I am fairly certain that many have not even gotten as far as installing it. Moreover, most of the potential issues do not manifest as a catastrophic failures, but are rather silent.</div>
<div style><br></div><div style>Additionally, the last few years I've had the opportunity to be in touch with sysadmins, programmers/engineers of HPC companies, experienced computational scientists, and similar advanced users and have seen their CMake cache and log files. These quite often showed signs of heavy compiler flag customization. Based on this experience, I can safely state that, this category of users does exists, and they do the kind of things that can be problematic with the new build system. Although they might not be great in numbers, I think I still it is not the best idea to ignore them, right?</div>
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<div>and adding or overriding should be possible through a single command-line invocation.<br>
<br>
More concretely IMO what we need is:<br>
- A summary printed or at least some read-only advanced variables so that one does not need to run e.g "mdrun -version" to know what flags are used;<br></div></div></div></div></div></div></blockquote></div><div>
I was (and still am) all for the summary. I really liked Teemu's start of it. But it got cut because of time. Not sure it would be a good idea to print just the flags without having a full summary. I think having read-only variables is very confusing.</div>
</div></div></div></blockquote><div><br></div></div><div>I see your point, but you have yet to reply to my criticism on the fact that <i>it is impossible to at least check what flags are being used</i> and that is a major flaw.<br>
</div></div></div></div></blockquote><div><br></div></div><div>CMake printing a summary seems awkward to me. If it's written as a status message, you can't see it with ccmake, and if it's written as a warning ccmake users will get in the habit of skipping real warnings. If using cmake, we'd want logic to only print such summary information for the final iteration - not sure if that's possible/easy enough to do.</div>
</div></blockquote><div><br></div><div style>Printing a summary after the first time configuring succeeds should be quite simple do do - that's how the GPU-related notes are issued when GPUs are detected in the build machine but CUDA is not found.</div>
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<div><br></div><div>However, a make target to print the configuration seems to address most of the issue. It replaces some of the use cases for inspecting config.log one might have with autoconf build systems. Yes, you'd have to run a normal cmake to find out the default (whether by a CMake summary or this make target I propose), then decide how to modify it, then apply it using some of the above mechanisms. If you magically know already what the defaults will be, you can skip the first stage already and jump straight to using GMX_SKIP_DEFAULT_CFLAGS. What do you think?</div>
</div></blockquote><div><br></div><div><div>I'd say we should print a configuration summary (with C/CXX/NVCC flags and the most important other options like fftw, CUDA, etc) both after the configure succeeds the first time as well as on user request.</div>
</div><div><br></div><div style>I think a target is a good idea, but I'm wondering whether a target is it more intuitive and/or easier to implement than having a cmake option that the user can turn on to get the summary printed.</div>
<div style><br></div><div style>To check the configuration on certain build directory which one of the following would you prefer?</div><div style><br></div><div style>$ make print-config-summary</div><div style><br></div>
<div style>$ cmake -DGMX_PRINT_CONFIG_SUMMARY</div><div style><br></div><div style> <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
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- An intuitive and consistent way to add/change the flags, what the user wants is simple, but currently requires a set of strange steps: enable skipping GROMACS flags, copy the printed flags, remove cache, re-run cmake with the copied flags.<br>
</div></div></div></div></div></div></blockquote></div><div>No need to remove the cache.</div></div></div></div></blockquote><div><br></div></div><div>Fine, remove that step, but you've to add two more instead:<br>- check default CMake flags;<br>
- re-add those when setting flags manually<br></div><div><br></div><div>Again, I would very much appreciate of you or others developers would actually comment on the issue in question: the usability concerns around this rather long, complicated, and error-prone set of steps required just to change a flag -Foo to -Bar.<br>
</div></div></div></div></blockquote><div><br></div></div><div>I was turned off by the tone of the original email. I imagine that has something to do with the low response rate so far. We've all been wrong at some point. Let's </div>
</div></blockquote><div><br></div><div style>I see you criticism and I was indeed a bit pissed in the beginning. Sorry for the rather pushy mail.</div><div style><br></div><div style>However, I still think that this major change in the build system behavior was merged in without much discussion, review, or feedback. The same is true for the closing of related bugs - if not both, at least 1040.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div class="gmail_quote"><div>start discussions by asking questions like "is there supposed to be a way for a user to add/replace/find out about a compiler flag?" If there isn't (or it isn't a </div>
</div></blockquote><div><br></div><div style>Again, you're right, I could have been a bit less judgmental. However, as I know our the build system fairly well and I am also somewhat familiar with cmake, I was quite certain that there is no robust workaround the issues raised.</div>
<div style> <br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div class="gmail_quote"><div>good solution) then discussion can move forward happily to solving the problem. If there is an existing solution, people are going to be happier to mention it if they don't feel like they have to defend their previous actions, or confront the asker by telling them they were wrong :-)</div>
</div></blockquote><div><br></div><div style>There isn't much to defend here, I think. This was *a* solution to a/some problem(s) which introduced a set of other problems. My tone and wording was not demanding because it was questioning the solution, but because I was questioning:</div>
<div style>i) whether introducing new issues was really appropriate/necessary;</div><div style>ii) merging and closing bugs hastily without much feedback.</div><div style><br></div><div style>Thanks Mark for taking the time to reply!</div>
<div style><br></div><div style>Cheers,</div><div style>--</div><div style>Szilárd</div><div style><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
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<div><br></div><div>Mark</div></font></span></div>
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