MPI on Windows: how to detect available library and processor count - windows

I would like to automate detection of an MPI library under Windows 10/11 via a script.
So far the only options would be MPICH2 or MS-MPI, so I'd like to:
Find an available installation (search for mpiexec.exe or spmd.exe)
For this, I'm currently running
# where mpiexec
C:\Program Files\Microsoft MPI\Bin\mpiexec.exe
and I can search for "Microsoft MPI" or "MPICH2" in the path string, but that's certainly not a general approach.
Detect the available number of CPUs on the local machine.
Is the following command general?
mpiexec -n *
Thanks of any help

I can search for "Microsoft MPI" or "MPICH2" in the path string, but that's certainly not a general approach.
There is no general approach on Windows (as opposed on Linux and MacOS). Programs can be installed everywhere though they are generally in:
C:\Program Files
C:\Program Files (x86)
C:\Users\YOUR_USER\AppData\...
An alternative solution is to search for a MPI program in the PATH. This solution require to modify the PATH in the system properties. There are Linux related tools to search programs in it like locate. Such tools can be executed from Windows using a Linux-friendly console (eg. Git-Bash, Cmder, etc.). Batch shell script are very limited and clearly not user-friendly. Powershell may have some similar feature (though it requires a Powershell console).
This is a mess since tools like CMake (which barely supports MPI) spend a lot of effort and runtime to search for many frequent locations so to search libraries with no guarantee.
Detect the available number of CPUs on the local machine.
In Powershell, you can use the following code:
$processor = Get-ComputerInfo -Property CsProcessors
$CPU_COUNT = $processor.CsProcessors.NumberOfCores
assuming you want to extract the number of core, or otherwise:
$processor = Get-ComputerInfo -Property CsProcessors
$CPU_COUNT = $processor.CsProcessors.NumberOfLogicalProcessors
assuming you want to extract the number of logical cores (ie. hyper-threads).
Whether you should use one or the other is dependent of your target application and the target machine. I advise to use the number of core.
An alternative solution is to use the hw-loc tool also available on Linux and portable on many platforms. It is also a great tool to understand, profile and control the platform configuration (especially on NUMA systems).
Note that using MPI on Windows is very uncommon these days. A lot of high-performance tools/libraries supports mainly Linux (and not Windows) since 100% of the top 500 supercomputers (meant to run MPI programs) operate on Linux.

Related

Finding the full path to an executable on Windows (more than a "which" equivalent)

I have a Powershell script on Win10 that needs to start multiple other programs, and finding that in a lot of cases I have to go looking for the full path to the executable file, and potentially hard-code that path in the script, which is not great for robustness or portability between machines.
On *nix systems, it is expected that most programs can be started from the command line, so each application will generally either add its install folder to the PATH environment variable, or be inserted (e.g. via symlinks) into a directory like /usr/bin that's already in the PATH.
Microsoft discourages the use of the PATH variable. Instead applications are SUPPOSED to insert a key for their main .exe file into one of two places in the registry, depending on whether the app is installed for one user or all users-
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\App Paths
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\App Paths
The (default) value under that key is the full path to the executable file.
(ref. https://learn.microsoft.com/en-us/windows/win32/shell/app-registration#finding-an-application-executable)
Except- it seems an awful lot of applications don't follow this recommendation. (Micrsoft's own PowerToys, Keepass2, FreeFileSync, Free Download Manager are just some examples).
These programs do (when not installed as portable apps) have a presence in the Registry, it's just not in the officially recommended places.
So, my question is- Is there an effective way to get a good (not necessarily perfect) general answer to the question "what is the full path to installed program X.exe" on Windows? at least where that program has saved a path somewhere in the registry.
This is similar to the question asked here- Equivalent of *Nix 'which' command in PowerShell? but with the important difference that I want to include "badly behaved" programs that don't correctly configure the PATH or the two registry keys described above.
Ideally this would be a function that could be called on the fly with the program name as a parameter that returns the pathname, but worst case if it requires a brute force search across the whole registry to find and then de-duplicate all the paths to .exe files under the %PROGRAMFILES% folders (64 and 32 bit), I guess I could run this once and save the result in a file as a hash table.
For MSI packages you could do:
$software = Get-CimInstance -Query "select Vendor,Name,Version,InstallLocation,Language from win32_product" | Select-Object -Property Vendor,Name,Version,InstallLocation,Language
Output:
This gives you at least the install location.
You may also take a look at get-StartApps, e.g.:
Get-StartApps | ?{$_.appid -match "\.exe"}

How do I get Windows to go as fast as Linux for compiling C++?

I know this is not so much a programming question but it is relevant.
I work on a fairly large cross platform project. On Windows I use VC++ 2008. On Linux I use gcc. There are around 40k files in the project. Windows is 10x to 40x slower than Linux at compiling and linking the same project. How can I fix that?
A single change incremental build 20 seconds on Linux and > 3 mins on Windows. Why? I can even install the 'gold' linker in Linux and get that time down to 7 seconds.
Similarly git is 10x to 40x faster on Linux than Windows.
In the git case it's possible git is not using Windows in the optimal way but VC++? You'd think Microsoft would want to make their own developers as productive as possible and faster compilation would go a long way toward that. Maybe they are trying to encourage developers into C#?
As simple test, find a folder with lots of subfolders and do a simple
dir /s > c:\list.txt
on Windows. Do it twice and time the second run so it runs from the cache. Copy the files to Linux and do the equivalent 2 runs and time the second run.
ls -R > /tmp/list.txt
I have 2 workstations with the exact same specs. HP Z600s with 12gig of ram, 8 cores at 3.0ghz. On a folder with ~400k files Windows takes 40seconds, Linux takes < 1 second.
Is there a registry setting I can set to speed up Windows? What gives?
A few slightly relevant links, relevant to compile times, not necessarily i/o.
Apparently there's an issue in Windows 10 (not in Windows 7) that closing a process holds a global lock. When compiling with multiple cores and therefore multiple processes this issue hits.
The /analyse option can adversely affect perf because it loads a web browser. (Not relevant here but good to know)
Unless a hardcore Windows systems hacker comes along, you're not going to get more than partisan comments (which I won't do) and speculation (which is what I'm going to try).
File system - You should try the same operations (including the dir) on the same filesystem. I came across this which benchmarks a few filesystems for various parameters.
Caching. I once tried to run a compilation on Linux on a RAM disk and found that it was slower than running it on disk thanks to the way the kernel takes care of caching. This is a solid selling point for Linux and might be the reason why the performance is so different.
Bad dependency specifications on Windows. Maybe the chromium dependency specifications for Windows are not as correct as for Linux. This might result in unnecessary compilations when you make a small change. You might be able to validate this using the same compiler toolchain on Windows.
A few ideas:
Disable 8.3 names. This can be a big factor on drives with a large number of files and a relatively small number of folders: fsutil behavior set disable8dot3 1
Use more folders. In my experience, NTFS starts to slow down with more than about 1000 files per folder.
Enable parallel builds with MSBuild; just add the "/m" switch, and it will automatically start one copy of MSBuild per CPU core.
Put your files on an SSD -- helps hugely for random I/O.
If your average file size is much greater than 4KB, consider rebuilding the filesystem with a larger cluster size that corresponds roughly to your average file size.
Make sure the files have been defragmented. Fragmented files cause lots of disk seeks, which can cost you a factor of 40+ in throughput. Use the "contig" utility from sysinternals, or the built-in Windows defragmenter.
If your average file size is small, and the partition you're on is relatively full, it's possible that you are running with a fragmented MFT, which is bad for performance. Also, files smaller than 1K are stored directly in the MFT. The "contig" utility mentioned above can help, or you may need to increase the MFT size. The following command will double it, to 25% of the volume: fsutil behavior set mftzone 2 Change the last number to 3 or 4 to increase the size by additional 12.5% increments. After running the command, reboot and then create the filesystem.
Disable last access time: fsutil behavior set disablelastaccess 1
Disable the indexing service
Disable your anti-virus and anti-spyware software, or at least set the relevant folders to be ignored.
Put your files on a different physical drive from the OS and the paging file. Using a separate physical drive allows Windows to use parallel I/Os to both drives.
Have a look at your compiler flags. The Windows C++ compiler has a ton of options; make sure you're only using the ones you really need.
Try increasing the amount of memory the OS uses for paged-pool buffers (make sure you have enough RAM first): fsutil behavior set memoryusage 2
Check the Windows error log to make sure you aren't experiencing occasional disk errors.
Have a look at Physical Disk related performance counters to see how busy your disks are. High queue lengths or long times per transfer are bad signs.
The first 30% of disk partitions is much faster than the rest of the disk in terms of raw transfer time. Narrower partitions also help minimize seek times.
Are you using RAID? If so, you may need to optimize your choice of RAID type (RAID-5 is bad for write-heavy operations like compiling)
Disable any services that you don't need
Defragment folders: copy all files to another drive (just the files), delete the original files, copy all folders to another drive (just the empty folders), then delete the original folders, defragment the original drive, copy the folder structure back first, then copy the files. When Windows builds large folders one file at a time, the folders end up being fragmented and slow. ("contig" should help here, too)
If you are I/O bound and have CPU cycles to spare, try turning disk compression ON. It can provide some significant speedups for highly compressible files (like source code), with some cost in CPU.
NTFS saves file access time everytime. You can try disabling it:
"fsutil behavior set disablelastaccess 1"
(restart)
The issue with visual c++ is, as far I can tell, that it is not a priority for the compiler team to optimize this scenario.
Their solution is that you use their precompiled header feature. This is what windows specific projects have done. It is not portable, but it works.
Furthermore, on windows you typically have virus scanners, as well as system restore and search tools that can ruin your build times completely if they monitor your buid folder for you. windows 7 resouce monitor can help you spot it.
I have a reply here with some further tips for optimizing vc++ build times if you're really interested.
The difficulty in doing that is due to the fact that C++ tends to spread itself and the compilation process over many small, individual, files. That's something Linux is good at and Windows is not. If you want to make a really fast C++ compiler for Windows, try to keep everything in RAM and touch the filesystem as little as possible.
That's also how you'll make a faster Linux C++ compile chain, but it is less important in Linux because the file system is already doing a lot of that tuning for you.
The reason for this is due to Unix culture:
Historically file system performance has been a much higher priority in the Unix world than in Windows. Not to say that it hasn't been a priority in Windows, just that in Unix it has been a higher priority.
Access to source code.
You can't change what you can't control. Lack of access to Windows NTFS source code means that most efforts to improve performance have been though hardware improvements. That is, if performance is slow, you work around the problem by improving the hardware: the bus, the storage medium, and so on. You can only do so much if you have to work around the problem, not fix it.
Access to Unix source code (even before open source) was more widespread. Therefore, if you wanted to improve performance you would address it in software first (cheaper and easier) and hardware second.
As a result, there are many people in the world that got their PhDs by studying the Unix file system and finding novel ways to improve performance.
Unix tends towards many small files; Windows tends towards a few (or a single) big file.
Unix applications tend to deal with many small files. Think of a software development environment: many small source files, each with their own purpose. The final stage (linking) does create one big file but that is an small percentage.
As a result, Unix has highly optimized system calls for opening and closing files, scanning directories, and so on. The history of Unix research papers spans decades of file system optimizations that put a lot of thought into improving directory access (lookups and full-directory scans), initial file opening, and so on.
Windows applications tend to open one big file, hold it open for a long time, close it when done. Think of MS-Word. msword.exe (or whatever) opens the file once and appends for hours, updates internal blocks, and so on. The value of optimizing the opening of the file would be wasted time.
The history of Windows benchmarking and optimization has been on how fast one can read or write long files. That's what gets optimized.
Sadly software development has trended towards the first situation. Heck, the best word processing system for Unix (TeX/LaTeX) encourages you to put each chapter in a different file and #include them all together.
Unix is focused on high performance; Windows is focused on user experience
Unix started in the server room: no user interface. The only thing users see is speed. Therefore, speed is a priority.
Windows started on the desktop: Users only care about what they see, and they see the UI. Therefore, more energy is spent on improving the UI than performance.
The Windows ecosystem depends on planned obsolescence. Why optimize software when new hardware is just a year or two away?
I don't believe in conspiracy theories but if I did, I would point out that in the Windows culture there are fewer incentives to improve performance. Windows business models depends on people buying new machines like clockwork. (That's why the stock price of thousands of companies is affected if MS ships an operating system late or if Intel misses a chip release date.). This means that there is an incentive to solve performance problems by telling people to buy new hardware; not by improving the real problem: slow operating systems. Unix comes from academia where the budget is tight and you can get your PhD by inventing a new way to make file systems faster; rarely does someone in academia get points for solving a problem by issuing a purchase order. In Windows there is no conspiracy to keep software slow but the entire ecosystem depends on planned obsolescence.
Also, as Unix is open source (even when it wasn't, everyone had access to the source) any bored PhD student can read the code and become famous by making it better. That doesn't happen in Windows (MS does have a program that gives academics access to Windows source code, it is rarely taken advantage of). Look at this selection of Unix-related performance papers: http://www.eecs.harvard.edu/margo/papers/ or look up the history of papers by Osterhaus, Henry Spencer, or others. Heck, one of the biggest (and most enjoyable to watch) debates in Unix history was the back and forth between Osterhaus and Selzer http://www.eecs.harvard.edu/margo/papers/usenix95-lfs/supplement/rebuttal.html
You don't see that kind of thing happening in the Windows world. You might see vendors one-uping each other, but that seems to be much more rare lately since the innovation seems to all be at the standards body level.
That's how I see it.
Update: If you look at the new compiler chains that are coming out of Microsoft, you'll be very optimistic because much of what they are doing makes it easier to keep the entire toolchain in RAM and repeating less work. Very impressive stuff.
I personally found running a windows virtual machine on linux managed to remove a great deal of the IO slowness in windows, likely because the linux vm was doing lots of caching that Windows itself was not.
Doing that I was able to speed up compile times of a large (250Kloc) C++ project I was working on from something like 15 minutes to about 6 minutes.
Incremental linking
If the VC 2008 solution is set up as multiple projects with .lib outputs, you need to set "Use Library Dependency Inputs"; this makes the linker link directly against the .obj files rather than the .lib. (And actually makes it incrementally link.)
Directory traversal performance
It's a bit unfair to compare directory crawling on the original machine with crawling a newly created directory with the same files on another machine. If you want an equivalent test, you should probably make another copy of the directory on the source machine. (It may still be slow, but that could be due to any number of things: disk fragmentation, short file names, background services, etc.) Although I think the perf issues for dir /s have more to do with writing the output than measuring actual file traversal performance. Even dir /s /b > nul is slow on my machine with a huge directory.
I'm pretty sure it's related to the filesystem. I work on a cross-platform project for Linux and Windows where all the code is common except for where platform-dependent code is absolutely necessary. We use Mercurial, not git, so the "Linuxness" of git doesn't apply. Pulling in changes from the central repository takes forever on Windows compared to Linux, but I do have to say that our Windows 7 machines do a lot better than the Windows XP ones. Compiling the code after that is even worse on VS 2008. It's not just hg; CMake runs a lot slower on Windows as well, and both of these tools use the file system more than anything else.
The problem is so bad that most of our developers that work in a Windows environment don't even bother doing incremental builds anymore - they find that doing a unity build instead is faster.
Incidentally, if you want to dramatically decrease compilation speed in Windows, I'd suggest the aforementioned unity build. It's a pain to implement correctly in the build system (I did it for our team in CMake), but once done automagically speeds things up for our continuous integration servers. Depending on how many binaries your build system is spitting out, you can get 1 to 2 orders of magnitude improvement. Your mileage may vary. In our case I think it sped up the Linux builds threefold and the Windows one by about a factor of 10, but we have a lot of shared libraries and executables (which decreases the advantages of a unity build).
How do you build your large cross platform project?
If you are using common makefiles for Linux and Windows you could easily degrade windows performance by a factor of 10 if the makefiles are not designed to be fast on Windows.
I just fixed some makefiles of a cross platform project using common (GNU) makefiles for Linux and Windows. Make is starting a sh.exe process for each line of a recipe causing the performance difference between Windows and Linux!
According to the GNU make documentation
.ONESHELL:
should solve the issue, but this feature is (currently) not supported for Windows make. So rewriting the recipes to be on single logical lines (e.g. by adding ;\ or \ at the end of the current editor lines) worked very well!
IMHO this is all about disk I/O performance. The order of magnitude suggests a lot of the operations go to disk under Windows whereas they're handled in memory under Linux, i.e. Linux is caching better. Your best option under windows will be to move your files onto a fast disk, server or filesystem. Consider buying an Solid State Drive or moving your files to a ramdisk or fast NFS server.
I ran the directory traversal tests and the results are very close to the compilation times reported, suggesting this has nothing to do with CPU processing times or compiler/linker algorithms at all.
Measured times as suggested above traversing the chromium directory tree:
Windows Home Premium 7 (8GB Ram) on NTFS: 32 seconds
Ubuntu 11.04 Linux (2GB Ram) on NTFS: 10 seconds
Ubuntu 11.04 Linux (2GB Ram) on ext4: 0.6 seconds
For the tests I pulled the chromium sources (both under win/linux)
git clone http://github.com/chromium/chromium.git
cd chromium
git checkout remotes/origin/trunk
To measure the time I ran
ls -lR > ../list.txt ; time ls -lR > ../list.txt # bash
dir -Recurse > ../list.txt ; (measure-command { dir -Recurse > ../list.txt }).TotalSeconds #Powershell
I did turn off access timestamps, my virus scanner and increased the cache manager settings under windows (>2Gb RAM) - all without any noticeable improvements. Fact of the matter is, out of the box Linux performed 50x better than Windows with a quarter of the RAM.
For anybody who wants to contend that the numbers wrong - for whatever reason - please give it a try and post your findings.
Try using jom instead of nmake
Get it here:
https://github.com/qt-labs/jom
The fact is that nmake is using only one of your cores, jom is a clone of nmake that make uses of multicore processors.
GNU make do that out-of-the-box thanks to the -j option, that might be a reason of its speed vs the Microsoft nmake.
jom works by executing in parallel different make commands on different processors/cores.
Try yourself an feel the difference!
I want to add just one observation using Gnu make and other tools from MinGW tools on Windows: They seem to resolve hostnames even when the tools can not even communicate via IP. I would guess this is caused by some initialisation routine of the MinGW runtime. Running a local DNS proxy helped me to improve the compilation speed with these tools.
Before I got a big headache because the build speed dropped by a factor of 10 or so when I opened a VPN connection in parallel. In this case all these DNS lookups went through the VPN.
This observation might also apply to other build tools, not only MinGW based and it could have changed on the latest MinGW version meanwhile.
I recently could archive an other way to speed up compilation by about 10% on Windows using Gnu make by replacing the mingw bash.exe with the version from win-bash
(The win-bash is not very comfortable regarding interactive editing.)

alternative bash for windows / or help on cygwin with specific tasks

my goal: to create a suite of scripts that do some common system tasks, which include these
copy/move/list/search/grep files
watch/start/stop processes
run queries against Oracle via sqlplus
i grew accustomed to using Cygwin/bash to ease my life at work, and frankly speaking, i don't want to move away from bash language and start learning PowerShell, for example - so i started searching for a way to run bash scripts on Windows, ... preferably something alternative to Cygwin.
the truth is that i am still not pleased with Cygwin installation, and the fact that there is no simple way around it, that it is targeting more or less expert users, and there are a number of things that might pop up during the installation. i mean. what i am trying to do now is to write a suite of scripts that will target someone less expert than me (and i am in no way a real expert) - in most cases some kind of an administrator who doesn't want to know the script details.
i am thinking that this user will also want to be able to run these scripts on another machine, and i want to be able to explain him/her how to do it, without just saying, call the support, and, me, eventually (so that we can install cygwin on another machine etc etc.)
i tried MinGW(msys) but it also needs manual steps to set things up - i mean, these manual steps have become something of a de facto standard in these Windows ports (sorry, maybe i have a mood for bragging). win-bash looked like it could be a solution, but i ended up trashing it too, because of the old bash version, and its inability to do things i was able to do in cygwin - specifically
here documents
things like "cmd /C dir *" (don't know why) - and yes, i do cmd /C dir in cases i am in some kind of shared network folder with thousands of files, and ls is significantly slower than dir
my questions at last:
am i doomed to use PowerShell? i guess i will, reluctantly, if i have to
is there a simple pre-packaged "slim" cygwin installation.. or, portable cygwin, even better? there is a cygwin-portable project on sourceforge, but it's not that doesn't need those manual steps, again, apparently - is there a way to automate those steps, perhaps? and if there is, i wonder why somebody hasn't done it already? - and then, would it be possible to call bash scripts from Windows command prompt using a simple command like "bash somescript.sh"?
thanks for your attention.
As mentioned here, the Cygwin installation can totally be scripted and parametrized to ran in a silently and automatic mode.
If you define the minimal list of cygwin packages you need, just use a little .bat script that call the cygmin setup executable like this
setup.exe --packages=list_of_packages_you_need --quiet-mode
If you wrap the cygwin install process, it should be tolerable for a less technical user.
The cygwin install can be streamlined using command-line args;
http://sources.redhat.com/ml/cygwin-apps/2003-03/msg00526.html
You can also automate the install of most cygwin packages through cyg-apt.
I haven't verified this but I suspect that msys implements a *nix look alike by creating windows executable versions of system commands. All of the common commands have an executable on my install of msys. If that is true then it should be possible to use them separate from a complete install.
Try copying "bash.exe", "cp.exe", etc. from the msys bin directory to a machine/vm that does not have an msys install and see if it works. You may need to copy some dll's or shared libraries as well. A windows dependency checker program would show which dll's an executable is using.
You could package up the stuff you use and make a simple installer or just copy the files with your scripts.
Take a look at MKS Toolkit. Unlike Cygwin, it can live within the Windows world. Files end in CR/LF like Windows files, and you don't have that /cygdrive/c stuff. Naked drive letters work fine in MKS Toolkit.
A few caveats:
I haven't used MKS Toolkit in a long time. See following reason.
MKS Toolkit is (sit down for this) $600 per license. Ouch! That's why I use Cygwin even though I don't think it's as good or works as well.
It's Kornshell based and not Bash (although this may be a bit different). Kornshell and BASH are 95% alike. However, that last 5% gets you. I actually like Kornshell better than BASH in many respects. Kornshell has the print statement which is way superior than the echo statement. Variable names don't disappear in blocks. You can easily do double loops because almost all the commands can take unit numbers of input and output. However, Kornshell doesn't have those neat escape characters in the prompt, and it's hard to find the exit status of a command in the middle of the pipeline.

Issue with Visual C++ 2010 (Express) External Tools command

I posted this on SuperUser...but I was hoping the pros here at SO might have a good idea about how to fix this as well....
Normally we develop in VS 2005 Pro, but I wanted to give VS 2010 a spin. We have custom build tools based off of GNU make tools that are called when creating an executable.
This is the error that I see whenever I call my external tool:
...\gnu\make.exe): *** couldn't commit memory for cygwin heap, Win32 error 487
The caveat is that it still works perfectly fine in VS2005, as well as being called straight from the command line. Also, my external tool is setup exactly the same as in VS 2005.
Is there some setting somewhere that could cause this error to be thrown?
From problem with heap, win32 error 487 :
Each Cygwin app gets a special heap
area to hold stuff which is inherited
to child processes. Eg. all file
descriptor structures are stored in
that heap area (called the "cygheap").
The cygheap has room for at least 4000
file descriptor structures. But -
that's the clue - it's fixed size. The
cygheap can't grow. It's size is
reserved at the application's start
and it's blocks are commited on
demand.
For some reason your server
application needs all the cygheap
space when running under the described
conditions.
A possible solution might be found in Changing Cygwin's Maximum Memory:
Cygwin's heap is extensible. However,
it does start out at a fixed size and
attempts to extend it may run into
memory which has been previously
allocated by Windows. In some cases,
this problem can be solved by adding
an entry in the either the
HKEY_LOCAL_MACHINE (to change the
limit for all users) or
HKEY_CURRENT_USER (for just the
current user) section of the registry.
Add the DWORD value heap_chunk_in_mb
and set it to the desired memory limit
in decimal MB. It is preferred to do
this in Cygwin using the regtool
program included in the Cygwin
package. (For more information about
regtool or the other Cygwin utilities,
see the section called “Cygwin
Utilities” or use the --help option of
each util.) You should always be
careful when using regtool since
damaging your system registry can
result in an unusable system. This
example sets memory limit to 1024 MB:
regtool -i set /HKLM/Software/Cygwin/heap_chunk_in_mb 1024
regtool -v list /HKLM/Software/Cygwin
Exit all running Cygwin processes and
restart them. Memory can be allocated
up to the size of the system swap
space minus any the size of any
running processes. The system swap
should be at least as large as the
physically installed RAM and can be
modified under the System category of
the Control Panel.
It wouldn't hurt to ensure that the maximum size of your windows swap file is large enough.
To summerize : The environment doesn't allocate enough heap space for the cygwin executables. For some reason the problem is more acute with VS2010 Express. You need to either fix the environment, or use another Linux port than cygwin, or use Microsoft utilities.
From the cygwin email lists it looks like other people have run into similar situations, even when not running via Visual Studio, to which they've found that the solution is often to play with Cygwin's maximum memory settings:
http://www.cygwin.com/cygwin-ug-net/setup-maxmem.html
(note: it's worth reading this conversation, from above, about some values that did and didn't work).
Others have also reported issues with Anti-Virus software (recommendation is to unload from memory for some reason), and possibly also compatibility settings (try with it set to XP) which can affect cygwin in certain cases. See: http://www.avrfreaks.net/index.php?name=PNphpBB2&file=viewtopic&p=377066
As for Visual Studio: Are you on a 64bit machine and if so are you usually running the tool in a 64bit environment?
I've found that because Visual Studio 2010 runs in 32bit, tools launched from it are launched as 32bit processes (for a good illustration of this, add "cmd" as a tool). I'm not sure why this wouldn't be affected on 2005 (unless 2005 lets the system launch the process (64bit) and 2010 handles it itself (32bit)).

Does a cross-platfrom compiler that can compile a native executable that can be run both in linux windows exist? Could it exist?

I remember a few years ago(2002) there was a multipartite virus that could be run natively on linux and windows. I don't know if a compiler could be specially craft an executable so that it could be read as both ELF and PE, so that the os would start executing at different entry points. Or a program that could merge two programs, one compiled using mingw, one compiled in native linux, to one program.
I don't know if such a program exists, or could it exist, and I'm know this could be implemented in Java or some scripting language, but that's not a native program.
Imagine the possibilities, I could deploy a program with linux and window (and perhaps os/x)libraries, and one main executable that could be run on any os. The cross-platform support would compensate the bigger size.
Windows programs have a DOS stub in the beginning, and I just ran an ELF executable through debug.com, which said that the first instruction of this exe was JG 0x147. Just maybe something could be done with this...
No.
Windows and Linux use vastly different binary file formats. See Portable Executable (Windows) and Executable and Linkable Format (Linux).
Something like WINE will run Windows executables on Linux but that's not the same thing.
This is actually a really terrible idea for multiple reasons.
Cross-compiling across operating system boundaries is extremely difficult to do properly.
If you go for the second route (building separate PE binaries on Windows and ELF on Linux, and then somehow merging them) you have to maintain two machines, each running a different OS and the full build stack, and you'd have to make sure that you tested both versions separately before gluing them together.
Dynamic linking is already a pain to properly manage, on Windows and on Linux; static linking can generate binaries that are much more inconvenient to deal with than whatever imaginary benefits you get from providing one single file type to your end-user.
If you want to run the same binary executable file on multiple OSes, your options are Java, Mono, and potentially NativeClient, the browser plug-in Google's developing to work around the "webapps are too slow" problem.

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