Dear Midas and Rootana people,

We have tried to update our midas DAQ with the new TID definitions describe in https://midas.triumf.ca/elog/Midas/1871 

And we have noticed an incompatibility of this new definitions with Rootana when reading an XmlOdb in our offline analyzer. 

The problem comes from  the function FindArrayPath in XmlOdb.cxx and the comparison of bank type as strings.
Ex: comparing the strings "DWORD" and "UNINT32"

An naive solution would be to print the number associated to the type (ex: '6' for DWORD/UNINT32), but that would mean changing Rootana and Midas source code. Moreover, it does decrease the readability of the XmlOdb file. 


Thanks for your time.
Estelle

> Dear Midas and Rootana people,
> 
> We have tried to update our midas DAQ with the new TID definitions describe in https://midas.triumf.ca/elog/Midas/1871 
> 
> And we have noticed an incompatibility of this new definitions with Rootana when reading an XmlOdb in our offline analyzer. 
> 
> The problem comes from  the function FindArrayPath in XmlOdb.cxx and the comparison of bank type as strings.
> Ex: comparing the strings "DWORD" and "UNINT32"
> 
> An naive solution would be to print the number associated to the type (ex: '6' for DWORD/UNINT32), but that would mean changing Rootana and Midas source code. Moreover, it does decrease the readability of the XmlOdb file. 
> 

Hi, it is unfortunate that a change was made in MIDAS that is incompatible with existing analysis software. I shall update the ROOTANA package to deal with this ASAP.

K.O.

In the DEAP experiment, the normal MIDAS mlogger gzip compression  is not fast enough for some data 
taking modes, so I am doing tests of other compression programs. Here is the results.

Executive summary:

fastest compression is no compression (cat at 1800 Mbytes/sec - memcpy speed), next best are:
"lzf" at 300 Mbytes/sec and  "lzop" at 250 Mbytes/sec with 50% compression
"gzip -1" at around 70 Mbytes/sec with around 70% compression
"bzip2" at around 12 Mbytes/sec with around 80% compression
"pbzip2", as advertised, scales bzip2 compression linearly with the number of CPUs to 46 Mbytes/sec (4 
real CPUs), then slower to a maximum 60 Mbytes/sec (8 hyper-threaded CPUs).

This confirms that our original choice of "gzip -1" method for compression using zlib inside mlogger is 
still a good choice. bzip2 can gain an additional 10% compression at the cost of 6 times more CPU 
utilization. lzo/lzf can do 50% compression at GigE network speed and at "normal" disk speed.

I think these numbers make a good case for adding lzo/lzf compression to mlogger.

Comments about the data:

- time measured is the "elapsed" time of the compression program. it excludes the time spent flushing 
the compressed output file to disk.
- the relevant number is the first rate number (input data rate)
- test machine has 32GB of RAM, so all I/O is cached, disk speed does not affect these results
- "cat" gives a measure of overall machine "speed" (but test file is too small to give precise measurement)
- "gzip -1" is the recommended MIDAS mlogger compression setting
- "pbzip2 -p8" uses 8 "hyper-threaded" CPUs, but machine only has 4 "real" CPU cores

<pre>
cat                 : time   0.2s, size    431379371    431379371, comp   0%, rate 1797M/s 1797M/s
cat                 : time   0.6s, size   1013573981   1013573981, comp   0%, rate 1809M/s 1809M/s
cat                 : time   1.1s, size   2027241617   2027241617, comp   0%, rate 1826M/s 1826M/s

gzip -1             : time   6.4s, size    431379371    141008293, comp  67%, rate  67M/s  22M/s
gzip                : time  30.3s, size    431379371    131017324, comp  70%, rate  14M/s   4M/s
gzip -9             : time  94.2s, size    431379371    133071189, comp  69%, rate   4M/s   1M/s

gzip -1             : time  15.2s, size   1013573981    347820209, comp  66%, rate  66M/s  22M/s
gzip -1             : time  29.4s, size   2027241617    638495283, comp  69%, rate  68M/s  21M/s

bzip2 -1            : time  34.4s, size    431379371     91905771, comp  79%, rate  12M/s   2M/s
bzip2               : time  33.9s, size    431379371     86144682, comp  80%, rate  12M/s   2M/s
bzip2 -9            : time  34.2s, size    431379371     86144682, comp  80%, rate  12M/s   2M/s

pbzip2 -p1          : time  34.9s, size    431379371     86152857, comp  80%, rate  12M/s   2M/s (1 CPU)
pbzip2 -p1 -1       : time  34.6s, size    431379371     91935441, comp  79%, rate  12M/s   2M/s
pbzip2 -p1 -9       : time  34.8s, size    431379371     86152857, comp  80%, rate  12M/s   2M/s

pbzip2 -p2          : time  17.6s, size    431379371     86152857, comp  80%, rate  24M/s   4M/s (2 CPU)
pbzip2 -p3          : time  11.9s, size    431379371     86152857, comp  80%, rate  36M/s   7M/s (3 CPU)
pbzip2 -p4          : time   9.3s, size    431379371     86152857, comp  80%, rate  46M/s   9M/s (4 CPU)
pbzip2 -p4          : time  45.3s, size   2027241617    384406870, comp  81%, rate  44M/s   8M/s
pbzip2 -p8          : time  33.3s, size   2027241617    384406870, comp  81%, rate  60M/s  11M/s

lzop -1             : time   1.6s, size    431379371    213416336, comp  51%, rate 261M/s 129M/s
lzop                : time   1.7s, size    431379371    213328371, comp  51%, rate 249M/s 123M/s
lzop                : time   4.3s, size   1013573981    515317099, comp  49%, rate 234M/s 119M/s
lzop                : time   7.3s, size   2027241617    978374154, comp  52%, rate 277M/s 133M/s
lzop -9             : time 176.6s, size    431379371    157985635, comp  63%, rate   2M/s   0M/s

lzf                 : time   1.4s, size    431379371    210789363, comp  51%, rate 299M/s 146M/s
lzf                 : time   3.6s, size   1013573981    523007102, comp  48%, rate 282M/s 145M/s
lzf                 : time   6.7s, size   2027241617    972953255, comp  52%, rate 303M/s 145M/s

lzma -0             : time  27s, size    431379371    112406964, comp  74%, rate  15M/s   4M/s
lzma -1             : time  35s, size    431379371    111235594, comp  74%, rate  12M/s   3M/s
lzma: > 5 min, killed

xz -0               : time  28s, size    431379371    112424452, comp  74%, rate  15M/s   4M/s
xz -1               : time  35s, size    431379371    111252916, comp  74%, rate  12M/s   3M/s
xz: > 5 min, killed
</pre>

Columns are:
compression program
time: elapsed time of the compression program (excludes the time to flush output file to disk)
size: size of input file, size of output file
comp: compression ration (0%=no compression, 100%=file compresses into nothing)
rate: input data rate (size of input file divided by elapsed time), output data rate (size of output file 
divided by elapsed time)

Machine used for testing (from /proc/cpuinfo):
Intel(R) Core(TM) i7-3820 CPU @ 3.60GHz
quad core cpu with hyper-threading (8 CPU total)
32 GB quad-channel DDR3-1600.

Script used for testing:

#!/usr/bin/perl -w

my $x = join(" ", @ARGV);

my $in  = "test.mid";
my $out = "test.mid.out";
my $tout = "test.time";

my $cmd = "/usr/bin/time -o $tout -f \"%e\" /usr/bin/time $x < test.mid > test.mid.out";

print $cmd,"\n";

my $t0 = time();
system $cmd;
my $t1 = time();

my $c = `cat $tout`;
print "Elapsed time: $c";

my $t = $c;

#system "/bin/ls -l $in $out";

my $sin  = -s $in;
my $sout = -s $out;

my $xt = $t1-$t0;
$xt = 1 if $xt<1;

print "Total time: $xt\n";

print sprintf("%-20s: time %5.1fs, size %12d %12d, comp %3.0f%%, rate %3dM/s %3dM/s", $x, $t, $sin, 
$sout, 100*($sin-$sout)/$sin, ($sin/$t)/1e6, ($sout/$t)/1e6), "\n";

exit 0;
# end

Typical output:

[deap@deap00 pet]$ ./r.perl lzf    
/usr/bin/time -o test.time -f "%e" /usr/bin/time lzf < test.mid > test.mid.out
1.27user 0.15system 0:01.44elapsed 99%CPU (0avgtext+0avgdata 2800maxresident)k
0inputs+411704outputs (0major+268minor)pagefaults 0swaps
Elapsed time: 1.44
Total time: 3
lzf                 : time   1.4s, size    431379371    210789363, comp  51%, rate 299M/s 146M/s

K.O.

I redid the tests from Konstantin for our MEG experiment at PSI. The event structure is different, so it
is interesting how the two different experiments compare. We have an event size of 2.4 MB and a trigger
rate of ~10 Hz, so we produce a raw data rate of 24 MB/sec. A typical run contains 2000 events, so has a 
size of 5 GB. Here are the results:


cat                 : time   7.8s, size   4960156030   4960156030, comp   0%, rate 639M/s 639M/s

gzip -1             : time 147.2s, size   4960156030   2468073901, comp  50%, rate  33M/s  16M/s

pbzip2 -p1          : time 679.6s, size   4960156030   1738127829, comp  65%, rate   7M/s   2M/s (1 CPU)
pbzip2 -p8          : time  96.1s, size   4960156030   1738127829, comp  65%, rate  51M/s  18M/s (8 CPU)


As one can see, our compression ratio is poorer (due to the quasi random noise in our waveforms), but the
difference between gzip -1 and pbzip2 is larger (15% instead 10% for DEAP). The single CPU version of
pbzip cannot sustain our DAQ rate of 24 MB, but the parallel version can. Actually we have a somehow old
dual-core dual-CPU board 2.5 GHz Xenon box, and make 8 hyper-threading CPUs out of the total 4 cores.
Interestingly the compression rate scales with 7.3 for 8 virtual cores, so hyper-threading does its job.
So we take all our data with the pbzip2 compression. The additional 15% as compared with gzip does 
not sound much, but we produce raw 250 TB/year. So gzip gives us 132 TB/year and pbzip2 gives 
us 98 TB/year, and we save quite some disks.

Note that you can run bzip2 (as all the other methods) already now with the current logger, if you specify
an external compression program in the ODB using the pipe functionality:


local:MEG:S]/>cd Logger/Channels/0/Settings/
[local:MEG:S]Settings>ls
Active                          y
Type                            Disk
Filename                        |pbzip2>/megdata/run%06d.mid.bz2
Format                          MIDAS
Compression                     0
ODB dump                        y
Log messages                    0
Buffer                          SYSTEM
Event ID                        -1
Trigger mask                    -1
Event limit                     0
Byte limit                      0
Subrun Byte limit               0
Tape capacity                   0
Subdir format                   
Current filename                /megdata/run197090.mid.bz2
</pre>

cc -c -g -O2 -Wall -Wuninitialized -Iinclude -Idrivers -I../mxml -Llinux/lib -DINCLUDE_FTPLIB   -D_LARGEFILE64_SOURCE -DHAVE_MYSQL -DHAVE_ROOT -pthread -I/opt/root/current/include -DOS_LINUX -fPIC -Wno-unused-function -o linux/lib/system.o src/system.c
src/system.c:958: error: expected declaration specifiers or ‘...’ before ‘gettid’
src/system.c:958: warning: data definition has no type or storage class
src/system.c:958: warning: type defaults to ‘int’ in declaration of ‘_syscall0’
src/system.c: In function ‘ss_gettid’:
src/system.c:1005: warning: implicit declaration of function ‘gettid’
src/system.c: In function ‘ss_suspend_init_ipc’:
src/system.c:2948: warning: pointer targets in passing argument 3 of ‘getsockname’ differ in signedness
src/system.c: In function ‘ss_suspend’:
src/system.c:3414: warning: pointer targets in passing argument 6 of ‘recvfrom’ differ in signedness
src/system.c:3441: warning: pointer targets in passing argument 6 of ‘recvfrom’ differ in signedness
make: *** [linux/lib/system.o] 错误 1

void ss_force_single_thread()
{
   _single_thread = TRUE;
}

#if defined(OS_DARWIN)
// blank
#elif defined(OS_LINUX)
_syscall0(pid_t,gettid);
#endif

INT ss_gettid(void)

/opt/DAQ/bot/midas/src/history_odbc.cxx: In member function 'virtual int 
SqlODBC::GetNumRows()':
/opt/DAQ/bot/midas/src/history_odbc.cxx:589: error: cannot convert 'SQLINTEGER*' 
to 'long int*' for argument '2' to 'SQLRETURN SQLRowCount(void*, long int*)'
/opt/DAQ/bot/midas/src/history_odbc.cxx: In member function 'virtual const char* 
SqlODBC::GetColumn(int)':
/opt/DAQ/bot/midas/src/history_odbc.cxx:638: error: cannot convert 'SQLINTEGER*' 
to 'long int*' for argument '6' to 'SQLRETURN SQLGetData(void*, SQLUSMALLINT, 
SQLSMALLINT, void*, long int, long int*)'
make[2]: *** [CMakeFiles/midas-static.dir/src/history_odbc.cxx.o] Error 1
make[2]: Leaving directory `/opt/DAQ/bot/midas/build'
make[1]: *** [CMakeFiles/midas-static.dir/all] Error 2
make[1]: Leaving directory `/opt/DAQ/bot/midas/build'

Hi all, 

I have updated our daq computer to the latest OS 10.15 with the idea that then I will get all our daq 
programs running and will not need to update again in years to come. 
But now I am running unto even more problems trying to compile Midas. 
OS 10.15.3, Xcode 11.3 with commad line tools 

Darrens-Mac-mini:~ betacage$ cd packages/midas/build/
Darrens-Mac-mini:build betacage$ cmake .. 
-- MIDAS: cmake version: 3.16.3
-- The C compiler identification is AppleClang 11.0.0.11000033
-- The CXX compiler identification is AppleClang 11.0.0.11000033
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- MIDAS: CMAKE_INSTALL_PREFIX: /Users/betacage/packages/midas
-- MIDAS: Found ROOT version 6.18/04
-- Found ZLIB: /usr/lib/libz.dylib  
-- MIDAS: Found ZLIB version 
-- MIDAS: Found OpenSSL version 1.1.1d
-- MIDAS: MySQL not found
-- MIDAS: ODBC not found
-- MIDAS: SQLITE not found
-- MIDAS: nvidia-smi not found
-- Found Git: /usr/bin/git (found version "2.21.0 (Apple Git-122.2)") 
-- MIDAS example/experiment: MIDAS in-tree-build
-- MIDAS: Found ZLIB version 
-- MIDAS example/experiment: Found ROOT version 6.18/04
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/betacage/packages/midas/build
Darrens-Mac-mini:build betacage$ make install
[  1%] Building CXX object CMakeFiles/mfeo.dir/src/mfe.cxx.o
In file included from /Users/betacage/packages/midas/src/mfe.cxx:15:
In file included from /Users/betacage/packages/midas/include/mfe.h:13:
/Users/betacage/packages/midas/include/midas.h:159:10: fatal error: 'pthread.h' file not found
#include <pthread.h>
         ^~~~~~~~~~~
1 error generated.
make[2]: *** [CMakeFiles/mfeo.dir/src/mfe.cxx.o] Error 1
make[1]: *** [CMakeFiles/mfeo.dir/all] Error 2


I guess that I am maybe the first one trying to install MIDAS in this OS, so I am willing to help as much as I 
can with getting this going. I have found a solution to this by downgrading Xcode to version 10 
https://stackoverflow.com/questions/58524715/failing-to-compile-a-c-application-under-macos-catalina-10-15
If you don't have other solutions I will try to do that tomorrow.

Thanks 

Berta 

> I have updated our daq computer to the latest OS 10.15 ...

FWIW, I do not have macos 10.15. I have 10.13 at home and 10.14 in the office. Maybe Stefan has it?

> In file included from /Users/betacage/packages/midas/include/mfe.h:13:
> /Users/betacage/packages/midas/include/midas.h:159:10: fatal error: 'pthread.h' file not found
> #include <pthread.h>
>          ^~~~~~~~~~~

Hmm... pthread.h should be there, I do not see any notice of it's removal in macos.

So I suspect a mis-installation of c++ compilers. In the past we had problems with this,
in addition to installing Xcode from the app store, one most install some missing stuff
manually ("XCode command line tools"), if I have it right, the command is "xcode-select --install".

If you figure out how to build it, I think midas will work just fine on the latest macos.

K.O.

> > I have updated our daq computer to the latest OS 10.15 ...
> 
> FWIW, I do not have macos 10.15. I have 10.13 at home and 10.14 in the office. Maybe Stefan has it?

No, I'm stuck with 10.14 due to the current lack of 64-bit support of some programs.

I would try KOs proposal to do a "xcode-select --install".

Stefan

> > > I have updated our daq computer to the latest OS 10.15 ...
> > 
> > FWIW, I do not have macos 10.15. I have 10.13 at home and 10.14 in the office. Maybe Stefan has it?
> 
> No, I'm stuck with 10.14 due to the current lack of 64-bit support of some programs.
> 

Ok, in this case, I will update my office mac mini to 10.15.

K.O.

> 
> Ok, in this case, I will update my office mac mini to 10.15.
> 
> K.O.


Hi Konstantin, 

Any luck with Midas in OS 10.15? 
I have downgraded to Xcode 10.2.1 as suggested in the post linked in my first post, without any luck, I keep getting the same pthead.h error. 
MY gcc uses the 10.15 sdk despite having v 10.2.1 for Xcode and command line tools 

Darrens-Mac-mini:~ betacage$ gcc --version
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-
dir=/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/c++/4.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
Target: x86_64-apple-darwin19.3.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin


and that is where I suspect the problem is. Will keep investigating next week. Thanks for your help.

Berta 

> Any luck with Midas in OS 10.15? 

Best I can tell, the problem is not in midas: pthread.h should be there, somewhere.

K.O.

> > Any luck with Midas in OS 10.15? 
> 
> Best I can tell, the problem is not in midas: pthread.h should be there, somewhere.
> 
> K.O.


HI Konstain, 

Thanks for your reply. I have been investigating this issue of pthread in OS 10.15.  Found this forum post 
https://github.com/wjakob/nori/issues/16

that seem to suggest that pthread.h is in a different directory from OS 10.14 and on. And the end of the post the 
developer suggests that he has found a way to fix the Cmake to work so I have checked his code updates in here 
https://github.com/wjakob/nori/commit/be46cccc01a75b21dad1a3f61baa108fe644fc4b

I have added his lines 


if(APPLE)
   # Try to auto-detect a suitable SDK
   execute_process(COMMAND bash -c "xcodebuild -version -sdk | grep MacOSX | grep Path | head -n 1 | cut -f 2 -
d ' '" OUTPUT_VARIABLE CMAKE_OSX_SYSROOT)
   string(REGEX REPLACE "(\r?\n)+$" "" CMAKE_OSX_SYSROOT "${CMAKE_OSX_SYSROOT}")
   string(REGEX REPLACE "^.*X([0-9.]*).sdk$" "\\1" CMAKE_OSX_DEPLOYMENT_TARGET 
"${CMAKE_OSX_SYSROOT}")
 endif()

to my local pakages/midas/CMakeLists.txt and run cmake .., make install again but now I get a different error 

[  1%] Building CXX object CMakeFiles/mfeo.dir/src/mfe.cxx.o
clang: error: invalid version number in '-mmacosx-version-
min=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/DriverKit19.0.sdk'
clang: warning: using sysroot for 'DriverKit' but targeting 'MacOSX' [-Wincompatible-sysroot]


I will continue investigating this issue tomorrow, but please let me know if you have any suggestions.

Also my version of cmake is 3.16.3

Thanks 

Berta 

For your reference, here on my MacOSX 10.14.6 with XCode 11.3.1 the pthread.h file is present in locations listed below.

Did you execute "xcode-select --install" ?


~$ locate pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/AppleTVOS.platform/Developer/SDKs/AppleTVOS.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/AppleTVOS.platform/Developer/SDKs/AppleTVOS.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/AppleTVSimulator.platform/Developer/SDKs/AppleTVSimulator.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/AppleTVSimulator.platform/Developer/SDKs/AppleTVSimulator.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/WatchOS.platform/Developer/SDKs/WatchOS.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/WatchOS.platform/Developer/SDKs/WatchOS.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/WatchSimulator.platform/Developer/SDKs/WatchSimulator.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/WatchSimulator.platform/Developer/SDKs/WatchSimulator.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/usr/include/pthread.h
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/pthread/pthread.h
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/pthread.h

> For your reference, here on my MacOSX 10.14.6 with XCode 11.3.1 the pthread.h file is present in locations listed below.
> 
> Did you execute "xcode-select --install" ?
> 
> 
> ~$ locate pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/AppleTVOS.platform/Developer/SDKs/AppleTVOS.sdk/usr/include/pthread/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/AppleTVOS.platform/Developer/SDKs/AppleTVOS.sdk/usr/include/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/AppleTVSimulator.platform/Developer/SDKs/AppleTVSimulator.sdk/usr/include/pthread/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/AppleTVSimulator.platform/Developer/SDKs/AppleTVSimulator.sdk/usr/include/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/pthread/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/WatchOS.platform/Developer/SDKs/WatchOS.sdk/usr/include/pthread/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/WatchOS.platform/Developer/SDKs/WatchOS.sdk/usr/include/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/WatchSimulator.platform/Developer/SDKs/WatchSimulator.sdk/usr/include/pthread/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/WatchSimulator.platform/Developer/SDKs/WatchSimulator.sdk/usr/include/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/include/pthread/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/include/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/usr/include/pthread/pthread.h
> /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/usr/include/pthread.h
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/pthread/pthread.h
> /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/pthread.h

Hi Stefan,

Thanks for looking into this. Yes, I have done  "xcode-select --install"

This is my output when I try to locate pthread.h

Darrens-Mac-mini:~ betacage$ locate pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/AppleTVOS.platform/Developer/SDKs/AppleTVOS.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/AppleTVOS.platform/Developer/SDKs/AppleTVOS.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/AppleTVSimulator.platform/Developer/SDKs/AppleTVSimulator.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/AppleTVSimulator.platform/Developer/SDKs/AppleTVSimulator.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/WatchOS.platform/Developer/SDKs/WatchOS.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/WatchOS.platform/Developer/SDKs/WatchOS.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/WatchSimulator.platform/Developer/SDKs/WatchSimulator.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/WatchSimulator.platform/Developer/SDKs/WatchSimulator.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk/usr/include/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/usr/include/pthread/pthread.h
/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/usr/include/pthread.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/pthread/pthread.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/pthread.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/pthread/pthread.h
/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include/pthread.h

and this is what I see in my SDKs folder 

Darrens-Mac-mini:SDKs betacage$ pwd
/Library/Developer/CommandLineTools/SDKs
Darrens-Mac-mini:SDKs betacage$ ls
MacOSX.sdk	MacOSX10.14.sdk	MacOSX10.15.sdk

So it looks like in this computer one needs to read the version of the SDK as pthread.h is not in MacOSX.sdk but in MacOSX10.15.sdk

Thanks 

Berta 

Another thought: Can you delete the build directory and run cmake again? Like

$ cd /midas/build
$ rm -rf *
$ cmake ..

If you have the old build cache and upgraded the OS in meantime, the cache needs to be rebuild.

Stefan

Another thought: Can you delete the midas build directory and run cmake again? Like

$ cd midas/build
$ rm -rf *
$ cmake ..
$ make VERBOSE=1

If you have the old build cache and upgraded your OS in meantime, the cache needs to be rebuild. The VERBOSE 
flag tells you the compiler options, and you see where the compiler looks for the SDK directory.

Cheers,
Stefan

> Another thought: Can you delete the midas build directory and run cmake again? Like
> 
> $ cd midas/build
> $ rm -rf *
> $ cmake ..
> $ make VERBOSE=1
> 
> If you have the old build cache and upgraded your OS in meantime, the cache needs to be rebuild. The VERBOSE 
> flag tells you the compiler options, and you see where the compiler looks for the SDK directory.
> 
> Cheers,
> Stefan

Hi Stefan, 

Thanks again for your reply. Yes! the suggestion of rebuilding the cache was the right one, this is the output of cmake ..

Darrens-Mac-mini:~ betacage$ cd packages/midas/build/
Darrens-Mac-mini:build betacage$ rm -rf *
Darrens-Mac-mini:build betacage$ cmake ..
-- MIDAS: cmake version: 3.16.3
-- The C compiler identification is AppleClang 11.0.0.11000033
-- The CXX compiler identification is AppleClang 11.0.0.11000033
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- MIDAS: CMAKE_INSTALL_PREFIX: /Users/betacage/packages/midas
-- MIDAS: Found ROOT version 6.18/04
-- Found ZLIB: /usr/lib/libz.dylib (found version "1.2.11") 
-- MIDAS: Found ZLIB version 1.2.11
-- Found OpenSSL: /usr/lib/libcrypto.dylib (found version "1.1.1d")  
-- MIDAS: Found OpenSSL version 1.1.1d
-- MIDAS: MySQL not found
-- MIDAS: ODBC not found
-- MIDAS: SQLITE not found
-- MIDAS: nvidia-smi not found
-- Setting default build type to "RelWithDebInfo"
-- Found Git: /usr/bin/git (found version "2.21.1 (Apple Git-122.3)") 
-- MIDAS example/experiment: MIDAS in-tree-build
-- MIDAS: Found ZLIB version 1.2.11
-- MIDAS example/experiment: Found ROOT version 6.18/04
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/betacage/packages/midas/build


Unfortunately running make VERBOSE=1 the compilation crashes, with the following error 

[ 39%] Linking CXX executable mhttpd
cd /Users/betacage/packages/midas/build/progs && /Applications/CMake.app/Contents/bin/cmake -E cmake_link_script CMakeFiles/mhttpd.dir/link.txt 
--verbose=1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++  -O2 -g -DNDEBUG -isysroot 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk -Wl,-search_paths_first -Wl,-
headerpad_max_install_names  CMakeFiles/mhttpd.dir/mhttpd.cxx.o CMakeFiles/mhttpd.dir/mongoose6.cxx.o CMakeFiles/mhttpd.dir/mgd.cxx.o 
CMakeFiles/mhttpd.dir/__/mscb/src/mscb.cxx.o  -o mhttpd  ../libmidas.a /usr/lib/libssl.dylib /usr/lib/libcrypto.dylib -lz 
ld: cannot link directly with dylib/framework, your binary is not an allowed client of /usr/lib/libcrypto.dylib for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [progs/mhttpd] Error 1
make[1]: *** [progs/CMakeFiles/mhttpd.dir/all] Error 2
make: *** [all] Error 2


Libcrypto seems to be part of the OpenSSL, so I am back to the original problem again. I did install OpenSSL via MacPorts. 

I have found this tread regarding this problem. But have to go and pick up my kids from school, so I don't have time to investigate today.
https://stackoverflow.com/questions/58446253/xcode-11-ld-error-your-binary-is-not-an-allowed-client-of-usr-lib-libcrypto-dy

Thanks again for staying with me and for responding so promptly. 

Berta