Migrate-n-mpi problem

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wapello65

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Mar 24, 2014, 1:26:07 PM3/24/14
to migrate...@googlegroups.com, bee...@fsu.edu
Hello Peter,

I am an experienced Migrate user (3.3.2) but am having difficulty installing/configuring the Migrate-3.6.4 parallel version to run on my Mac. I have unpacked the archived file and copied the migrateshell.app to my Applications folder, per the README instructions. However, when I try to install the software, again according to the instructions, I receive the following message:

Patrick-Larkins-Computer-2:migrate-3.6.4 patricklarkin$ cd src
Patrick-Larkins-Computer-2:src patricklarkin$ ./configure
checking build system type... i686-apple-darwin11.4.2
checking host system type... i686-apple-darwin11.4.2
checking target system type... i686-apple-darwin11.4.2
checking for gmake... make
=======================================================================
Migrate subversion: 
Hardware: apple
System OS: darwin11.4.2  Darwin  -DGRANDCENTRAL
System CPU: i686
-----------------------------------------------------------------------
checking for gcc... no
checking for icc... no
checking for pgcc... no
checking for cc... no
configure: error: in `/Users/patricklarkin/desktop/migrate-3.6.4/src':
configure: error: no acceptable C compiler found in $PATH
See `config.log' for more details
Patrick-Larkins-Computer-2:src patricklarkin$ 

It seems to indicate I have no compiler capable of performing this function. I'm using a pretty standard Mac:

2.7 GHz Intel Core i5, 4 Cores
Mac OS Lion 10.7.5


I haven't noticed any similar messages in the support forum, so I can't tell if this is an issue with my computer or OS 10.7.5. I've read through the manual, README, README_ PARALLEL_GENERAL, and forum but all seem to assume that configuration/compiling steps operate normally.

BTW, Migrate-n seems to operate normally, using the executable file contained in the Migrate-3.6.4 directory.

 Any help would be appreciated. Thanks.

Patrick

Pablo G Goikoetxea

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Mar 26, 2014, 3:47:04 AM3/26/14
to migrate...@googlegroups.com
Hi Patrick
Is your experience with Migrate in a Mac or elsewhere? The compilers do not install by default in mac osX. You need to install the developers tools. I do not remember the actual package name, before they were called X-code.

Cheers
Pablo


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Peter Beerli

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Mar 26, 2014, 7:07:52 AM3/26/14
to migrate...@googlegroups.com
Patrick,
you will need Xcode on the mac and once you have installed look into the Preferences->Downloads and make sure that the command line utilities are checked. 
I also suggest to upgrade to MacOS 10.9 from your 10.7 installation. Looking back the macos 10.6 was great and the next good one is 10.9 (the current), for me 10..7 was a low point in terms of usability/stability. Of course you mileage may vary, if you stick with 10.7 make sure that your Xcode is compatible with that, there were a couple of sweeping changes within Xcode that may have led to problems with older OSes.

Peter

wapello65

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Apr 7, 2014, 6:02:23 PM4/7/14
to migrate...@googlegroups.com
Thank you Peter. I installed X-code and made sure the command line utilities were installed. I followed these instructions to successfully compile Migrate:

./configure
make
make clean
make mpis

I successfully ran the example file, after changing back to the EXAMPLE folder using the following command

mpirun -np 4 --host localhost ../src/migrate-n-mpi parmfile.testbayes

But I am now having problems analyzing my data. i see the migrate-n-mpi executable in my src directory. I move it one level up into the Migrate 3.6.4 directory and open it by double-clicking (the Migrate 3.6.4 directory is where I keep my input files). Migrate for parallel architecture opens normally, I set the options I desire but when i try to run it gives me the message "cannot read from input file", even though that input file is in that directory, and runs fine with migrate-n (single CPU version). I know this must be a simple command line problem but I do not have much experience is this area. Can you tell me what I'm doing wrong? 

Many thanks,

Patrick

Peter Beerli

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Apr 7, 2014, 10:43:34 PM4/7/14
to migrate...@googlegroups.com
Patrick
do not double click the migrate binary!
if your data and migrate-n-mpi is in the same directory then
cd to that directory
and execute the mpirun command, for example
your data is infile your parmfile is parmfile and you have all in the directory migrate-3.6.4 on your Desktop
cd
cd Desktop/migrate-3.6.4
mpirun -np 4 —host localhost ./migrate-n-mpi parmfile

cd moves you to your home directory
cd Desktop/migrate-3.6.4 moves you to the directory with the data and binary
the mpirun will then run your parmfile


Peter

wapello65

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Apr 8, 2014, 4:45:41 PM4/8/14
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Thank you Peter and Pablo,

This is now working. Thank you for your patience. I'm sure it's trying to constantly answer such basic command line questions.

Patrick

Milvago

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Jan 16, 2018, 3:40:43 PM1/16/18
to migrate-support
Dear migrate-n users, I need help with the "make mpis" command. I got this output that indicates an error at the very end. I am attempting to install migrate-n  on a MacOS High Sierra 3.4GHz intel Core i5.

¿Can you suggest anything that might help to complete installation?

Rauls-iMac:src Milvago$ make mpis

(cd ./haru ; make -f makefile.osx "CC=g++" "CPP=gcc" "ARCH=" "MACOSVERSION=" "MYCPPFLAGS=-DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER  ")

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfExceptions.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfList.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfUtils.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfStreams.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfAutoPtrObjects.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfObjects.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfContents.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfPages.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfFonts.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfXref.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfDestinations.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfOutlines.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfBorderStyle.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfAnnotations.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfDoc.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfCatalog.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfInfo.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfEncoding.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfFontDef.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfXObjects.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfFontDef_Courier.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfFontDef_Helvetica.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfFontDef_Times.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfFontDef_Symbol.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfFontDef_ZapfDingbats.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfEncoding_ISO8859.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfEncoding_KOI8.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfEncoding_MSCP.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfMbFonts.cc

PdfMbFonts.cc:260:9: warning: 'delete[]' applied to a pointer that was allocated with 'new'; did you mean 'delete'? [-Wmismatched-new-delete]

        delete[] w;

        ^     ~~

PdfMbFonts.cc:247:24: note: allocated with 'new' here

    pdf_cid_width* w = new pdf_cid_width;

                       ^

PdfMbFonts.cc:270:9: warning: 'delete[]' applied to a pointer that was allocated with 'new'; did you mean 'delete'? [-Wmismatched-new-delete]

        delete[] w;

        ^     ~~

PdfMbFonts.cc:247:24: note: allocated with 'new' here

    pdf_cid_width* w = new pdf_cid_width;

                       ^

PdfMbFonts.cc:300:9: warning: 'delete[]' applied to a pointer that was allocated with 'new'; did you mean 'delete'? [-Wmismatched-new-delete]

        delete[] w;

        ^     ~~

PdfMbFonts.cc:284:24: note: allocated with 'new' here

    pdf_cid_width* w = new pdf_cid_width;

                       ^

PdfMbFonts.cc:311:9: warning: 'delete[]' applied to a pointer that was allocated with 'new'; did you mean 'delete'? [-Wmismatched-new-delete]

        delete[] w;

        ^     ~~

PdfMbFonts.cc:284:24: note: allocated with 'new' here

    pdf_cid_width* w = new pdf_cid_width;

                       ^

4 warnings generated.

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfCMap.cc

PdfCMap.cc:207:9: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]

        delete btype;

        ^

              []

PdfCMap.cc:175:28: note: allocated with 'new[]' here

    pdf_byte_type* btype = new pdf_byte_type[srclen];

                           ^

PdfCMap.cc:210:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]

    delete btype;

    ^

          []

PdfCMap.cc:175:28: note: allocated with 'new[]' here

    pdf_byte_type* btype = new pdf_byte_type[srclen];

                           ^

2 warnings generated.

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfUnicodeText.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfMbFontDef_Gothic.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfMbFontDef_Mincyo.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfMbFontDef_SimHei.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfMbFontDef_SimSun.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfMbFontDef_Ming.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfMbFontDef_Batang.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfMbFontDef_Dotum.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfCMap_RKSJ.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfCMap_EUC.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfCMap_GB_EUC.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfCMap_ETen_B5.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfCMap_KSCms_UHC.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfCMap_KSC_EUC.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfPngImage.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfJpegImage.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c PdfEncrypt.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c libharuc.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c libharuc_jpfonts.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c libharuc_krfonts.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c libharuc_cnsfonts.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c libharuc_cntfonts.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c libharu_png.cc

gcc   -I.  -DNDEBUG -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER    -c libharu_jpeg.cc

ar rc libharu.a PdfExceptions.o PdfList.o PdfUtils.o PdfStreams.o PdfAutoPtrObjects.o PdfObjects.o PdfContents.o PdfPages.o PdfFonts.o PdfXref.o PdfDestinations.o PdfOutlines.o PdfBorderStyle.o PdfAnnotations.o PdfDoc.o PdfCatalog.o PdfInfo.o PdfEncoding.o PdfFontDef.o PdfXObjects.o PdfFontDef_Courier.o PdfFontDef_Helvetica.o PdfFontDef_Times.o PdfFontDef_Symbol.o PdfFontDef_ZapfDingbats.o PdfEncoding_ISO8859.o PdfEncoding_KOI8.o PdfEncoding_MSCP.o PdfMbFonts.o PdfCMap.o PdfUnicodeText.o PdfMbFontDef_Gothic.o PdfMbFontDef_Mincyo.o PdfMbFontDef_SimHei.o PdfMbFontDef_SimSun.o PdfMbFontDef_Ming.o PdfMbFontDef_Batang.o PdfMbFontDef_Dotum.o PdfCMap_RKSJ.o PdfCMap_EUC.o PdfCMap_GB_EUC.o PdfCMap_ETen_B5.o PdfCMap_KSCms_UHC.o PdfCMap_KSC_EUC.o PdfPngImage.o PdfJpegImage.o PdfEncrypt.o libharuc.o libharuc_jpfonts.o libharuc_krfonts.o libharuc_cnsfonts.o libharuc_cntfonts.o libharu_png.o libharu_jpeg.o 

/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libharu.a(PdfPngImage.o) has no symbols

/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libharu.a(PdfJpegImage.o) has no symbols

/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libharu.a(PdfEncrypt.o) has no symbols

/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libharu.a(libharu_png.o) has no symbols

/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libharu.a(libharu_jpeg.o) has no symbols

ranlib libharu.a

/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libharu.a(PdfPngImage.o) has no symbols

/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libharu.a(PdfJpegImage.o) has no symbols

/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libharu.a(PdfEncrypt.o) has no symbols

/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libharu.a(libharu_png.o) has no symbols

/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libharu.a(libharu_jpeg.o) has no symbols

Using system zlib architecture

/Library/Developer/CommandLineTools/usr/bin/make migrate-n-mpi "CC=mpicc" "CFLAGS = -O3 -fvectorize  -funroll-loops -Di686    -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937   -DMIGRATESUBVERSION=\"\\\"June-18-15\\\"\"  -DMIGRATEVERSION=\"\\\"3.6.11\\\"\"  -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER  -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT" "LIBS = -Lharu -lharu -lstdc++  -lz -lm "

mpicc -O3 -fvectorize  -funroll-loops -Di686    -DNEXUSTREE -DHAVE_ZLIB -DZNZ -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP -DMERSENNE_TWISTER -DMEXP=19937   -DMIGRATESUBVERSION="\"June-18-15\""  -DMIGRATEVERSION="\"3.6.11\""  -DNOJPEG -DNOPNG  -Iharu -DPRETTY -DLETTERPAPER  -DMPI -DSLOWNET -DNEWREPLICANT -DMPIREPLICANT -c aic.c 

/bin/sh: mpicc: command not found

make[1]: *** [aic.o] Error 127

make: *** [mpis] Error 2

Peter Beerli

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Jan 16, 2018, 4:01:24 PM1/16/18
to migrate...@googlegroups.com
google openmpi and mac 
if you use homebrew you can use that to install openmpi
migrate will need that

Peter


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