Re: [migrate-support] installation on Mac and data file reading error

Peter Beerli

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Nov 30, 2012, 11:25:13 AM11/30/12

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On Nov 30, 2012, at 9:45 AM, bibek yumnam <bibek....@gmail.com> wrote:

Hi Peter,
I am running migrate-n3.3.1 (single processor version) on both a Mac and on a pc, and noticed a string of problems in both systems.
Q. How do i go about installing fastmigrate on a Mac system? The MacOS10.5.8 desktop I am currently using has multiple processors (16 cores). open.mpi is already present on the system

Q. My dataset comprises 163 individuals, 11 loci and 4 pops. I have finished a rather long ML run which lasted almost ten days on a pc and faced with a peculiar problem.
When comparing the infile and outfile, I noticed there is a problem with reading the genotype data. eg. in the infile,
eg. the genotype for loci 1 in sample D1598 is heterozygous (200 203) but is read as homozygous (15.15) in the outfile.
Another problem that is present is outfile concversion to pdf which does not work.

datafile on infile
4 11 Mig CI pops
#M 3 3 2 4 2 4 2 4 3 4 4
16 MTR
D1598 200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217
D1599 188.188 114.123 127.129 149.157 137.139 ?.? 171.171 266.270 211.211 144.144 225.225
D1622 188.209 120.123 129.129 149.157 144.146 155.164 171.180 266.266 211.214 ?.? 213.225

datafile on outfile
loci 1 2 3 4 5 6 7 8 9 10 11
indiv.
D1598 15.15 14.14 18.18 14.14 14.14 24.24 17.16 19.19 16.16 14.15 14.14
D1599 11.11 12.11 17.17 14.14 14.14 ?.?.?.? 12.12 20.20 16.16 15.14 16.16
D1622 11.11 13.13 18.18 14.14 17.17 19.18 12.12 20.20 16.17 ?.?.?.? 13.13

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Peter Beerli

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Nov 30, 2012, 2:48:41 PM11/30/12

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Bibek,

your datafile contains errors:

to use the brownian motion model you will need to tell migrate the spacer between the alleles,

your first four lines should look like this:

4 11 . Mig CI pops

#@M 3 3 2 4 2 4 2 4 3 4 4

16 MTR

D1598______200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217

where _ means a space you used a tab that may interfere sometimes, but the main problem is that migrate read

your column as one allele and not two and got later confused.

ty again and make sure to check (print also the data)

Peter

Peter Beerli

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Dec 2, 2012, 11:41:45 PM12/2/12

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Bibek,

I sent you this:

> 4 11 . Mig CI pops
> #@M 3 3 2 4 2 4 2 4 3 4 4
> 16 MTR
> D1598______200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217

[the ___ means to replace the tab character with spaces so that each individual has a total of 10 characters.]

you say you fixed with this:

> 4 11 . Mig CI pops

> # M 3 3 2 4 2 4 2 4 3 4 4

> 16 MTR
> D1598 200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217

I hope you see the difference in the character lengths of the individuals and the setting for the repeat lengths.
I also run your data fragment on my computer and there this gives correctly:

loci 1 2 3 4 5 6 7 8 9 10 11
indiv.

D1598 15.16 14.16 12.12 11.13 11.15 16.16 16.22 11.13 11.12 11.12 12.12
D1599 11.11 11.14 11.12 11.13 11.12 ?.? 11.11 12.13 11.11 11.11 14.14
D1622 11.18 13.14 12.12 11.13 15.15 11.13 11.15 12.12 11.12 ?.? 11.14

a different result to the one you show, could you tell me

- what type of operating system
- what version of migrate
- which mutation model do you use

if you use a recent version of migrate then it should work, if it does not then something is wrong but at the moment it is not clear what.

Peter

Peter Beerli

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Dec 3, 2012, 4:09:52 PM12/3/12

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Dear Bibek,

On Dec 3, 2012, at 3:45 PM, bibek yumnam <bibek....@gmail.com> wrote:

Hi Peter,
Great to get your reply and suggestions. I am using using migrate-n version 3.3.1 and running it on windows7 pro. the mutation model i have opted for my run is brownian
You are correct about the infile..i have used a altered version without @ for my run.
However the program is able to read the data correctly, but don't know in other way it could impact the run.

What do you mean with "but don't know in other way it could impact the run."

I have listed below four different types of infiles that I've tested.. nos 1 and 2 read the data correctly..but 3 and 4 cause problems in reading.
Thanks again,
Bibek

Case 1. with @ symbol and tab delimiter between sample ID and first allele

4 11 . Mig CI pops
#@M 3 3 2 4 2 4 2 4 3 4 4
16 MTR

D1598 200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217

D1599 188.188 114.123 127.129 149.157 137.139 ?.? 171.171 266.270 211.211 144.144 225.225

the data is read correctly in the form of a 2digit output

loci 1 2 3 4 5 6 7 8 9 10 11
indiv.

D1598 15.16 14.16 18.18 14.16 14.18 24.24 16.22 19.21 16.17 15.16 14.14
D1599 11.11 11.14 17.18 14.16 14.15 ?.? 11.12 20.21 16.16 15.15 16.16

CASE 1 is the almost correct way to format it (migrate tries to resolve the tab between the individual name and the microsatellite data and succeeds, in rare cases it fails to do so

[looks correct!]

however when i input it in the following way
Case 2. without @ symbol but keeping tab delimiter between sample ID and first allele

4 11 . Mig CI pops
# M 3 3 2 4 2 4 2 4 3 4 4
16 MTR
D1598 200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217

D1599 188.188 114.123 127.129 149.157 137.139 ?.? 171.171 266.270 211.211 144.144 225.225

the data is still read correctly but in the original 3 digit output

loci 1 2 3 4 5 6 7 8 9 10 11
indiv.

D1598 200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217

D1599 188.188 114.123 127.129 149.157 137.139 ?.? 171.171 266.270 211.211 144.144 225.225

CASE 2: this is correct behavior because the # is treated as a comment, only #@M and for historical reason #M will trigger the translation from fragment length to repeat numbers

you can add comment lines into the datafile using # as the very first character, to make sure it is read correctly migrate expects a blank after the # and then skips the line .

On the other hand, the data gets read wrongly in the following two cases 3 and 4, whetre in the infile space (and not tab) has been used as delimiter between the sample ID and the forst allele.

Case 3. with @ symbol and space delimiter between sample ID and first allele

4 11 . Mig CI pops
# M 3 3 2 4 2 4 2 4 3 4 4
16 MTR
D1598 200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217

D1599 188.188 114.123 127.129 149.157 137.139 ?.? 171.171 266.270 211.211 144.144 225.225

result

loci 1 2 3 4 5 6 7 8 9 10 11
indiv.

D1598 200. 16.16 14.16 13.13 13.15 12.15 17.17 17.23 19.21 12.13 15.16 14.14
D1599 188. 11.11 11.14 12.13 13.15 12.13 ?.? 12.12 20.21 12.12 14.14 16.16

CASE 3: are you sure in the datafile is that space between # and M (# M) [your, because the conversion should not be triggered in this case, but your text above says that you used #@M?

The problem is that you replaced the tab only with a single blank space, the individual name MUST add to 10 spaces and you your case migrate assumes the name is "D1598 200." thus

reads the data incorrectly.

Case 4. without @ symbol but keeping space delimiter between sample ID and first allele
infile

4 11 . Mig CI pops
# M 3 3 2 4 2 4 2 4 3 4 4
16 MTR
D1598 200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217

D1599 188.188 114.123 127.129 149.157 137.139 ?.? 171.171 266.270 211.211 144.144 225.225

outfile

loci 1 2 3 4 5 6 7 8 9 10 11
indiv.

D1598 200. 203.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217
D1599 188. 188.188 114.123 127.129 149.157 137.139 ?.? 171.171 266.270 211.211 144.144 225.225

CASE 4: same problem as above: The problem is that you replaced the tab only with a single blank space, the indiviudal name MUST add to 10 spaces and you your case migrate assumes the name is "D1598 200." thus

reads the data incorrectly.

Peter

On Friday, November 30, 2012 9:45:54 AM UTC-5, bibek yumnam wrote:

Hi Peter,
I am running migrate-n3.3.1 (single processor version) on both a Mac and on a pc, and noticed a string of problems in both systems.
Q. How do i go about installing fastmigrate on a Mac system? The MacOS10.5.8 desktop I am currently using has multiple processors (16 cores). open.mpi is already present on the system

Q. My dataset comprises 163 individuals, 11 loci and 4 pops. I have finished a rather long ML run which lasted almost ten days on a pc and faced with a peculiar problem.
When comparing the infile and outfile, I noticed there is a problem with reading the genotype data. eg. in the infile,
eg. the genotype for loci 1 in sample D1598 is heterozygous (200 203) but is read as homozygous (15.15) in the outfile.
Another problem that is present is outfile concversion to pdf which does not work.

datafile on infile
4 11 Mig CI pops

#M 3 3 2 4 2 4 2 4 3 4 4

16 MTR
D1598 200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217

D1599 188.188 114.123 127.129 149.157 137.139 ?.? 171.171 266.270 211.211 144.144 225.225
D1622 188.209 120.123 129.129 149.157 144.146 155.164 171.180 266.266 211.214 ?.? 213.225

datafile on outfile

loci 1 2 3 4 5 6 7 8 9 10 11
indiv.

D1598    15.15 14.14 18.18 14.14 14.14 24.24 17.16 19.19 16.16 14.15 14.14
D1599    11.11 12.11 17.17 14.14 14.14 ?.?.?.? 12.12 20.20 16.16 15.14 16.16
D1622    11.11 13.13 18.18 14.14 17.17 19.18 12.12 20.20 16.17 ?.?.?.? 13.13

On Friday, November 30, 2012 9:45:54 AM UTC-5, bibek yumnam wrote:

Hi Peter,
I am running migrate-n3.3.1 (single processor version) on both a Mac and on a pc, and noticed a string of problems in both systems.
Q. How do i go about installing fastmigrate on a Mac system? The MacOS10.5.8 desktop I am currently using has multiple processors (16 cores). open.mpi is already present on the system

Q. My dataset comprises 163 individuals, 11 loci and 4 pops. I have finished a rather long ML run which lasted almost ten days on a pc and faced with a peculiar problem.
When comparing the infile and outfile, I noticed there is a problem with reading the genotype data. eg. in the infile,
eg. the genotype for loci 1 in sample D1598 is heterozygous (200 203) but is read as homozygous (15.15) in the outfile.
Another problem that is present is outfile concversion to pdf which does not work.

datafile on infile
4 11 Mig CI pops

#M 3 3 2 4 2 4 2 4 3 4 4

16 MTR
D1598 200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217

D1599 188.188 114.123 127.129 149.157 137.139 ?.? 171.171 266.270 211.211 144.144 225.225
D1622 188.209 120.123 129.129 149.157 144.146 155.164 171.180 266.266 211.214 ?.? 213.225

datafile on outfile

loci 1 2 3 4 5 6 7 8 9 10 11
indiv.

D1598 15.15 14.14 18.18 14.14 14.14 24.24 17.16 19.19 16.16 14.15 14.14
D1599 11.11 12.11 17.17 14.14 14.14 ?.?.?.? 12.12 20.20 16.16 15.14 16.16
D1622 11.11 13.13 18.18 14.14 17.17 19.18 12.12 20.20 16.17 ?.?.?.? 13.13

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bibek yumnam

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Dec 3, 2012, 8:20:31 PM12/3/12

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Dear Peter,

just to clarify..there was a mistake in my message showing the infile i posted here for case3 ,,i did use #@M and not # M for the run

Case 3. with @ symbol and space delimiter between sample ID and first allele
4 11 . Mig CI pops

#@M 3 3 2 4 2 4 2 4 3 4 4
16 MTR
D1598 200.203 123.129 129.129 149.157 137.144 176.176 180.192 262.270 211.214 144.149 217.217
D1599 188.188 114.123 127.129 149.157 137.139 ?.? 171.171 266.270 211.211 144.144 225.225

there was a mistake in my message showing the infile i posted here for case3 ,,i did use #@M and not # M for the run

bibek yumnam

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Dec 4, 2012, 2:43:27 PM12/4/12

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Hi Peter,

Thanks for pointing out the mistakes i made with the data files... the program is reading the data correctly and the runs are going fine now on a windows pc..

I am however faced with an entirely different problem and hope you can throw light on it..For quite some time now, I am have been trying rather unsuccessfully to install fastmigrate on a MacOS10.5.8 desktop which has multiple 16 cores

openmpi-1.6.3 is installed on the system.but fastmigrate simply does not get installed.

Following are the error messages that i get..

1. This is the message i get when I open the migrate shell and type in install_migrate

Migrate:migrate-3.3.2>install_migrate

File "/Users/Bibek/Desktop/migrate-3.3.2/migrateshell.app/migrate_kit/install_migrate", line 20

except OSError as exc: # Python >2.5

^

SyntaxError: invalid syntax

Migrate:migrate-3.3.2>

2. When i open the migrate shell and type "fastmigrate-n" the following message appears

===================================================================

Shell to run the program MIGRATE-N

(website: popgen.sc.fsu.edu)

===================================================================

to run migrate use a command from below.

If the commands do not work send an email to me at

beerli at fsu.edu

This machine has 16 cores. With more than 1 core you can run

multiple loci or multiple replicates in parallel and get about a speed

improvement of 16 x.

Commands: Explanation:

about A short explanation on how the binaries were compiled

migrate-n Single CPU version using multiple cores

fastmigrate-n Multiple CPU/cores version [this computer has 16 ]

findcores Shows the number of available computer cores

migratehelp Shows ALL available commands

Migrate:migrate-3.3.2>install_openmpi

openmpi 1.6 is already installed

Migrate:migrate-3.3.2>fastmigrate-n

16 compute nodes and one director node

/Users/Bibek/Desktop/migrate-3.3.2/migrateshell.app/migrate_kit/.hostfile

/usr/local/openmpi-1.6/bin/mpirun

dyld: unknown required load command 0x80000022

/Users/Bibek/Desktop/migrate-3.3.2/migrateshell.app/migrate_kit/fastmigrate-n: line 16: 47220 Trace/BPT trap mpirun -v -x PATH -np $cores --hostfile $dir/hostfile migrate-n-mpi $1 $2

Migrate:migrate-3.3.2>findcores

16

Migrate:migrate-3.3.2>

3. typing "mpirun -np 3 migrate-n-mpi (my)parmfile" shows the exact error message

Migrate:test run 3.3.2>mpirun -np 3 migrate-n-mpi parmfile

dyld: unknown required load command 0x80000022

Trace/BPT trap

4. typing "mpirun -np 3 --host localhost migrate-n-mpi parmfile" also shows the exact message

Migrate:test run 3.3.2>mpirun -np 3 --host localhost migrate-n-mpi parmfile

dyld: unknown required load command 0x80000022

Trace/BPT trap

Migrate:test run 3.3.2>

I am utterly confused with what these messages mean and would really appreciate your advice in getting past this issue.

Thanks and regards,

Bibek

Peter Beerli

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Dec 4, 2012, 5:58:59 PM12/4/12

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Bibek,

the binary of the openmpi library are not compatible with your machine,

1. Do you have an INTEL cpu in your system or a PPC?

2. Which binary version of migrate did you download? The distributed 10.5.8 binary of migrate was compiled on an old PPC laptop.

3. Can you compile a program on your computer? try in a commandline:

gcc --version

you should see something like this below or "command not found"

i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)

This is free software; see the source for copying conditions. There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Peter

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bibek yumnam

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Dec 4, 2012, 10:30:46 PM12/4/12

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Peter,

I am unable to see your reply regarding the Mac installation ..the webpage gives a loading message but is unable to open

bibek yumnam

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Dec 5, 2012, 10:04:59 AM12/5/12

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Peter,

Thanks a lot for your suggestions...I can now see your response and also the email you had sent..

to answer your questions..

1. the cpu is 2 x 2.26 GHz Quad-core Intel Xeon

2. I downloaded migrate-3.3.2.MacOS1.6.tar.gz

3. I have already complied the program on the system but will try it again,,

will let you know how it works out,,

thanks again,

Bibek

bibek yumnam

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Dec 5, 2012, 11:26:48 AM12/5/12

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Peter,

Sorry to bother you again..I tried compiling migrate and the following is a logfile of what occurred.

the error message says that make file is absent..

Can you tell me if I am doing this correctly

Bibek

Last login: Wed Dec 5 10:47:15 on ttys001

NZP-MG89124T320G:~ Bibek$ /Users/Bibek/Desktop/migrate-3.3.2/src/./configure

checking build system type... i686-apple-darwin9.8.0

checking host system type... i686-apple-darwin9.8.0

checking target system type... i686-apple-darwin9.8.0

checking for gmake... make

=======================================================================

Migrate subversion:

Hardware: apple

System OS: darwin9.8.0 Darwin

System CPU: i686

-----------------------------------------------------------------------

checking for gcc... gcc

checking whether the C compiler works... yes

checking for C compiler default output file name... a.out

checking for suffix of executables...

checking whether we are cross compiling... no

checking for suffix of object files... o

checking whether we are using the GNU C compiler... yes

checking whether gcc accepts -g... yes

checking for gcc option to accept ISO C89... none needed

checking for g++... g++

checking whether we are using the GNU C++ compiler... yes

checking whether g++ accepts -g... yes

C-compiler: gcc

C++-compiler:g++

CFLAGS: -O3 -tree-vectorize -funroll-loops -fast -Di686

=======================================================================

checking for a BSD-compatible install... /usr/bin/install -c

checking for pthread_create in -lpthread... yes

checking for MPI_Init in -lmpi... yes

checking for exp in -lm... yes

checking how to run the C preprocessor... gcc -E

checking for grep that handles long lines and -e... /usr/bin/grep

checking for egrep... /usr/bin/grep -E

checking for ANSI C header files... yes

checking for sys/types.h... yes

checking for sys/stat.h... yes

checking for stdlib.h... yes

checking for string.h... yes

checking for memory.h... yes

checking for strings.h... yes

checking for inttypes.h... yes

checking for stdint.h... yes

checking for unistd.h... yes

checking limits.h usability... yes

checking limits.h presence... yes

checking for limits.h... yes

checking for strings.h... (cached) yes

checking pthread.h usability... yes

checking pthread.h presence... yes

checking for pthread.h... yes

checking for an ANSI C-conforming const... yes

checking for size_t... yes

checking for int... yes

checking whether struct tm is in sys/time.h or time.h... time.h

checking for inline... inline

checking return type of signal handlers... void

checking for strftime... yes

checking for strcspn... yes

checking for strsep... yes

checking for lgamma... yes

checking which zlib implementation to use... autodetect

checking for main in -lz... yes

checking for gzbuffer... no

sh: copy_mt_to_src: No such file or directory

configure: creating ./config.status

config.status: creating Makefile

config.status: creating conf.h

config.status: conf.h is unchanged

MIGRATE-N is now setup

to compile the program you need to type one of the

commands below (ordered by preference):

SINGLE CPU machines

make # with PDF output support

# this might fail on first attempt,

# if the make fails, please let me know

# often linking fails because the C++ pdf library

# and the core migrate parts (C) mismatch

# check the Makefile line for STDLIB= -lstdc++

SMP machines more than 1 CPU in machine

make thread # uses the thread library if present

make # on macs running macos 10.6+ using GrandCentral

PARALLEL Computers, Clusters with MPI software

make mpis # each cpu-core can be treated as a node

make mpis-thread # experimental, may increase load per node!

------------------------------------------------------------------------

SPEED and other TESTING

the migrate website contains a testsuite.tar.gz that has

many tests for single, parallel and thread compilations

the tests are driven by a python script rt (see the README

in the testsuite) and a submit script that allows to streamline

submissions to a batch queue system, currently supported systems

are SUN/ORACLE GRIDENGINE, TORQUE/MOAB, and NONE

------------------------------------------------------------------------

In case there are problems with the compile send a message to the

migrate...@google.com usergroup, include a log of

./configure

make

=======================================================================

NZP-MG89124T320G:~ Bibek$ make

-----------------------------------------------------

Migrate 3.3.2

please **read** the documentation

this Makefile will produce an executable: migrate-n

or migrate-n-mpi for the parallel version

For more Makefile options type make help

I am interested in getting email about any problems.

Please send all compile warning or error messages

to bee...@fsu.edu [Peter Beerli]

----------------------------------------------------

make all

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

/bin/sh: line 0: cd: ./haru: No such file or directory

make[2]: makefile.osx: No such file or directory

make[2]: *** No rule to make target `makefile.osx'. Stop.

make[1]: *** [haru] Error 2

make: *** [intro] Error 2

NZP-MG89124T320G:~ Bibek$ make all

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

/bin/sh: line 0: cd: ./haru: No such file or directory

make[1]: makefile.osx: No such file or directory

make[1]: *** No rule to make target `makefile.osx'. Stop.

make: *** [haru] Error 2

NZP-MG89124T320G:~ Bibek$ make install

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

/bin/sh: line 0: cd: ./haru: No such file or directory

make[1]: makefile.osx: No such file or directory

make[1]: *** No rule to make target `makefile.osx'. Stop.

make: *** [haru] Error 2

NZP-MG89124T320G:~ Bibek$ make thread

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

/bin/sh: line 0: cd: ./haru: No such file or directory

make[1]: makefile.osx: No such file or directory

make[1]: *** No rule to make target `makefile.osx'. Stop.

make: *** [haru] Error 2

NZP-MG89124T320G:~ Bibek$

Peter Beerli

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Dec 5, 2012, 11:41:31 AM12/5/12

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Bibek,

macos 10.5.8 is very different from 10.6, they are not really 100% library-binary compatible,

I think that running it on 10.5.8 is a mistake, I would at least upgrade to 10.6 because 10.6 is stable and still somewhat maintained by apple.

Peter

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Peter Beerli

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Dec 5, 2012, 11:44:10 AM12/5/12

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mmmmh,

download the source and not the binary directory [the newversions contain the brandnew 3.4 source], it seems that the source directory in the binary distribution is missing the haru directory

Peter

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bibek yumnam

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Dec 5, 2012, 12:20:21 PM12/5/12

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Peter,

Thanks a lot for the reply..

You're right..I should upgrade the OS to 10.6 ..

and yes, I did download the source file and not the binary as you had advised..

Anyways, no issue,,I still have the program running on windows.

Bibek

Peter Beerli

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Dec 5, 2012, 1:53:45 PM12/5/12

to migrate...@googlegroups.com

Here recipe to try:

curl http://popgen.sc.fsu.edu/newversions/migrate-3.4.src.tar.gz > migrate-3.4.src.tar.gz

tar xvfz migrate-3.4.src.tar.gz

cd migrate-3.4/src

configure

make mac

the make mac target will ask whether you are an admin of your computer, I guess that you are

it will install migrate-n, migrte-n-mpi into /usr/local/migrate/bin

and migrateshell.app into /Applications

and after that it should work (if you have openmpi installed -- otherwise the compile of the migrate-n-mpi will fail.

After this is done, look into your .bash_profile file there should be only a single entry that points towards /usr/local/migrate/bin

you will need to logout and login, after this.

bibek yumnam

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Dec 5, 2012, 4:28:39 PM12/5/12

to migrate...@googlegroups.com

Hi Peter,

Thanks for sending the recipe..

I just tried it out and no luck either

configure was not a problem..but make mac was

the haru folder is still showing the error.

this is what i got after and make mac

NZP-MG89124T320G:~ Bibek$ make mac

make migrateshell

make clean

make haru-clean

(cd ./haru ; make -f makefile.osx clean)

/bin/sh: line 0: cd: ./haru: No such file or directory

make[4]: makefile.osx: No such file or directory

make[4]: *** No rule to make target `makefile.osx'. Stop.

make[3]: *** [haru-clean] Error 2

make[2]: *** [clean] Error 2

make[1]: *** [migrateshell] Error 2

make: *** [mac] Error 2

NZP-MG89124T320G:~ Bibek$

bibek yumnam

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Dec 5, 2012, 4:33:02 PM12/5/12

to migrate...@googlegroups.com

Peter,

On a luckier note, I managed to find a Mac OS10.6.8 with 16 cores in the lab, which i am now trying to crank up for the program...

gcc is not working...so gotta fix that first with say Xcode 3.2 and then I will try to compile migrate on it..

hope it works,

Bibek

John Phillips

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Jan 30, 2017, 1:48:24 PM1/30/17

to migrate-support

Dr. Beerli,

Similar to the above thread I am having issues installing MIGRATE-n on my computer (Mac OS 10.7.5).

I got to Step #4 Make (pg. 83) in the manual.

My error seems similar to the issues Bibek was having (above), but the 'make mac' command yielded more errors as he found (I cannot see a solution on this feed). Any thoughts? (error messages below)

Thanks in advance!

-John

Johns-MacBook-Pro-2:src johnphillips$ make

-----------------------------------------------------

Migrate 3.6.11

please **read** the documentation

this Makefile will produce an executable: migrate-n

or migrate-n-mpi for the parallel version

For more Makefile options type make help

I am interested in getting email about any problems.

Please send all compile warning or error messages

to bee...@fsu.edu [Peter Beerli]

----------------------------------------------------

make all

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

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

In file included from /usr/include/c++/4.2.1/bits/os_defines.h:61,

from /usr/include/c++/4.2.1/bits/c++config.h:41,

from /usr/include/c++/4.2.1/exception:42,

from libharu.h:25,

from PdfExceptions.cc:17:

/usr/include/unistd.h:634: error: declaration of C function ‘void swab(void*, void*, ssize_t)’ conflicts with

/usr/include/string.h:172: error: previous declaration ‘void swab(const void*, void*, ssize_t)’ here

In file included from /usr/include/c++/4.2.1/bits/os_defines.h:61,

from /usr/include/c++/4.2.1/bits/c++config.h:41,

from /usr/include/c++/4.2.1/exception:42,

from libharu.h:25,

from PdfExceptions.cc:17:

/usr/include/unistd.h:690: error: declaration of C function ‘void _Exit(long int)’ conflicts with

/usr/include/stdlib.h:199: error: previous declaration ‘void _Exit(int)’ here

/usr/include/unistd.h:711: error: declaration of C function ‘long int mkstemp(char*)’ conflicts with

/usr/include/stdlib.h:218: error: previous declaration ‘int mkstemp(char*)’ here

/usr/include/unistd.h:731: error: declaration of C function ‘void setkey(char*)’ conflicts with

/usr/include/stdlib.h:235: error: previous declaration ‘void setkey(const char*)’ here

/usr/include/unistd.h:751: error: declaration of C function ‘long int getsubopt(char**, char**, char**)’ conflicts with

/usr/include/stdlib.h:206: error: previous declaration ‘int getsubopt(char**, char* const*, char**)’ here

In file included from PdfExceptions.cc:17:

libharu.h: In member function ‘virtual void PdfVirtualObject::InternalWriteStream(PdfStreamBase*, PdfEncryptor*)’:

libharu.h:1241: warning: deprecated conversion from string constant to ‘char*’

libharu.h:1243: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘virtual void PdfNullObject::InternalWriteStream(PdfStreamBase*, PdfEncryptor*)’:

libharu.h:1259: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘virtual void PdfBoolean::InternalWriteStream(PdfStreamBase*, PdfEncryptor*)’:

libharu.h:1279: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘void PdfDictionary::SetType(char*)’:

libharu.h:1529: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘PdfArray* PdfPages::Kids()’:

libharu.h:2204: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘char* PdfInfo::Author()’:

libharu.h:2659: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘char* PdfInfo::Creator()’:

libharu.h:2660: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘char* PdfInfo::Producer()’:

libharu.h:2661: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘char* PdfInfo::Title()’:

libharu.h:2662: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘char* PdfInfo::Subject()’:

libharu.h:2663: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘char* PdfInfo::Keywords()’:

libharu.h:2664: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘void PdfInfo::SetAuthorMb(char*, PdfCMap*)’:

libharu.h:2680: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘void PdfInfo::SetCreatorMb(char*, PdfCMap*)’:

libharu.h:2682: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘void PdfInfo::SetProducerMb(char*, PdfCMap*)’:

libharu.h:2684: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘void PdfInfo::SetTitleMb(char*, PdfCMap*)’:

libharu.h:2686: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘void PdfInfo::SetSubjectMb(char*, PdfCMap*)’:

libharu.h:2688: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘void PdfInfo::SetKeywordsMb(char*, PdfCMap*)’:

libharu.h:2690: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘PdfOutlineItem* PdfOutlineBase::First()’:

libharu.h:2750: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘PdfOutlineItem* PdfOutlineBase::Last()’:

libharu.h:2752: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘PdfOutlineItem* PdfOutlineItem::Prev()’:

libharu.h:2788: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘PdfOutlineItem* PdfOutlineItem::Next()’:

libharu.h:2790: warning: deprecated conversion from string constant to ‘char*’

libharu.h: In member function ‘PdfOutline* PdfOutlineItem::Parent()’:

libharu.h:2792: warning: deprecated conversion from string constant to ‘char*’

make[2]: *** [PdfExceptions.o] Error 1

make[1]: *** [haru] Error 2

make: *** [intro] Error 2

Johns-MacBook-Pro-2:src johnphillips$ make mac

make migrateshell

make clean

make haru-clean

(cd ./haru ; make -f makefile.osx clean)

/bin/rm -f *.o libharu.a libharu.so*

/bin/rm -f examples/*.o

/bin/rm -f examples/EncodingList examples/GraphPaper examples/FontExample1 examples/FontExample2 examples/LineExample examples/LinkExample examples/OutlineExample examples/PngExample examples/JpegExample examples/Encrypt examples/Permission examples/JpFontExample1 examples/JpFontExample2 examples/TextAnnotation

/bin/rm -rf *.o *.a gmon.out