Problem with update.sh

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yveeteyang
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Joined: May 21st, 2015, 6:05 am
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Problem with update.sh

Post by yveeteyang » December 12th, 2016, 7:18 am

Dear Forum,
I'm having trouble using update.sh after downloading code using wget(which I've just downloaded a few days ago), here is my problem.
Repository location (local, server):
server
Enter command (export, checkout, log, version):
checkout
./update.sh: line 31: svn: command not found
./update.sh: line 51: svn: command not found
mv: cannot stat `version1.inc': No such file or directory
mv: cannot stat `version2.inc': No such file or directory

Do you know where the problem is? Thank you for your help!

yveeteyang
Posts: 12
Joined: May 21st, 2015, 6:05 am
Registered HYSPLIT User: Yes

Re: Problem with update.sh

Post by yveeteyang » December 12th, 2016, 8:19 am

Also, since my compiler is intel fortran, I've changed the Makefile under /home/xxx/hysplit/trunk/library/hysplit and /trunk/exec, changing the compiler from gfortran to intel fortran by comment and uncomment those lines:
# fortran compilers and flags
# CFLAGS = $(GFOR)
# FC = gfortran
CFLAGS = $(INTL)
FC = ifort
# CFLAGS = $(PGF9)
# FC = pgf90
is that right?
and then I run compile.sh under trunk directory, now I get this:
dos2unix: converting file mayo_pm25.txt to UNIX format ...
dos2unix: converting file smkrun.bat to UNIX format ...
dos2unix: converting file smkrun.sh to UNIX format ...
Building fcsubs library
Building hysplit source library
Building lbfgsb source library
Building exec directory programs
ERROR

Would you tell me where the problem lies? Thank you very much!

ariel.stein
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Re: Problem with update.sh

Post by ariel.stein » December 12th, 2016, 10:15 am

The first problem you have is that you do not have svn installed. Please install svn.
The second problem you have is that you are mixing compilers in your Makefiles. You will have to go under each of the following directories and change the compiler in the makefiles from gfortran to ifortran: library/hysplit ; library/lbfgsb ; and exec

yveeteyang
Posts: 12
Joined: May 21st, 2015, 6:05 am
Registered HYSPLIT User: Yes

Re: Problem with update.sh

Post by yveeteyang » December 12th, 2016, 11:32 am

Thank you for your help, I've followed your suggestion and changed the compiler in all those three, but now I get errors like this:
dos2unix: converting file smkrun.sh to UNIX format ...
Building fcsubs library
Building hysplit source library
ERROR

And I went to see the compile.log, at the end of this file it shows:
make[1]: ifort: Command not found
make[1]: *** [member] Error 127
make[1]: Leaving directory `/home/yyj/hysplit/trunk/library/hysplit'
make[1]: Entering directory `/home/yyj/hysplit/trunk/library/hysplit'
ifort -c -O -FR -diag-disable 8290,8291 -assume byterecl -convert big_endian -I. gemtst.f
make[1]: ifort: Command not found
make[1]: *** [member] Error 127
make[1]: Leaving directory `/home/yyj/hysplit/trunk/library/hysplit'
make: *** [../libhysplit.a] Error 2

It seems worse than last time, would you please help me find out what happened? Thanks.
ariel.stein wrote:The first problem you have is that you do not have svn installed. Please install svn.
The second problem you have is that you are mixing compilers in your Makefiles. You will have to go under each of the following directories and change the compiler in the makefiles from gfortran to ifortran: library/hysplit ; library/lbfgsb ; and exec

ariel.stein
Posts: 606
Joined: November 7th, 2012, 3:14 pm
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Re: Problem with update.sh

Post by ariel.stein » December 12th, 2016, 12:12 pm

Do you have ifortran installed?

yveeteyang
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Re: Problem with update.sh

Post by yveeteyang » December 12th, 2016, 9:44 pm

Yes, My server has intel fortran installed, version 10.
ariel.stein wrote:Do you have ifortran installed?

ariel.stein
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Re: Problem with update.sh

Post by ariel.stein » December 13th, 2016, 10:04 am

well, according to the error you are getting you do not have ifort in your path
"ifort: Command not found"

Please make sure you can call ifort from the hysplit directories.

yveeteyang
Posts: 12
Joined: May 21st, 2015, 6:05 am
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Re: Problem with update.sh

Post by yveeteyang » December 13th, 2016, 12:04 pm

i tried again and it's the same problem as before, it stopped at building exec directory programs, and I went to see the compile.log it showed:
lbfgsb.f:(.text+0xacc1): undefined reference to `_gfortran_st_write'
lbfgsb.f:(.text+0xacd0): undefined reference to `_gfortran_st_write_done'
lbfgsb.f:(.text+0xb6ac): undefined reference to `_gfortran_st_write'
lbfgsb.f:(.text+0xb6c5): undefined reference to `_gfortran_transfer_character'
lbfgsb.f:(.text+0xb6d4): undefined reference to `_gfortran_st_write_done'
lbfgsb.f:(.text+0xb70c): undefined reference to `_gfortran_st_write'
lbfgsb.f:(.text+0xb725): undefined reference to `_gfortran_transfer_character'
lbfgsb.f:(.text+0xb734): undefined reference to `_gfortran_st_write_done'
lbfgsb.f:(.text+0xbbfa): undefined reference to `_gfortran_st_write'
lbfgsb.f:(.text+0xbc09): undefined reference to `_gfortran_st_write_done'
../library/liblbfgsb.a(lbfgsb.o): In function `dcsrch_':
lbfgsb.f:(.text+0xbc6a): undefined reference to `_gfortran_compare_string'
lbfgsb.f:(.text+0xc01b): undefined reference to `_gfortran_compare_string'
lbfgsb.f:(.text+0xc612): undefined reference to `_gfortran_compare_string'
lbfgsb.f:(.text+0xc635): undefined reference to `_gfortran_compare_string'
../library/liblbfgsb.a(timer.o): In function `timer_':
timer.f:(.text+0x2e): undefined reference to `_gfortran_cpu_time_4'
make: *** [lbfgsb] Error 1

I've changed the Makefile in three directories as you mentioned, so what's the problem now? Thank you so much.
ariel.stein wrote:well, according to the error you are getting you do not have ifort in your path
"ifort: Command not found"

Please make sure you can call ifort from the hysplit directories.

ariel.stein
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Re: Problem with update.sh

Post by ariel.stein » December 13th, 2016, 2:12 pm

OK, it seems you mixed your compilers when you did your original compilations.
Please go to each directory and do a "make clean". That would get rid of all the libraries that you created with gfortran.
Next, go to each of the directories and type "make". The last make should be done in the exec directory.

yveeteyang
Posts: 12
Joined: May 21st, 2015, 6:05 am
Registered HYSPLIT User: Yes

Re: Problem with update.sh

Post by yveeteyang » December 19th, 2016, 2:13 am

I just download the source code and do everything all over again, and now the problem seems to do with my netCDF, my version is 4.1.1.
I changed the Makefile in /cmaq, /exec,/library/hysplit,library/lbfgsb and /data2arl/arw2arl, to make the compilers from gfortran to ifort like this:

#CFLAGS = $(GFOR)
#FC = gfortran
CFLAGS = $(INTL)
FC = ifort

And I also changed the Makefile in /cmaq and in data2arl/arw2arl as my netCDF is not installed to /usr/local, here is my code:
in /cmaq:
# IOAPI LIBRARY
API = /home/yaoyu/netCDF/lib

# exported in calling script
NETLIB = /home/yaoyu/netCDF/lib
NETINC = /home/yaoyu/netCDF/include
# NETINC = /usr/local/include
# NETLIB = /usr/local/lib

# library name for netCDF3=netcdf and for netCDF4=netcdff
# LINKS = -L$(NETLIB) -lnetcdf -L../library -lhysplit
LINKS = -L$(NETLIB) -lnetcdff -L../library -lhysplit

in /arw2arl:
# exported in calling script
NETLIB = /home/yaoyu/netCDF/lib
NETINC = /home/yaoyu/netCDF/include
# NETLIB = /usr/local/lib
# NETINC = /usr/local/include

# library name for netCDF3=netcdf and for netCDF4=netcdff
# LINKS = -L$(NETLIB) -lnetcdf -L../../library -lhysplit
LINKS = -L$(NETLIB) -lnetcdff -L../../library -lhysplit

And after doing all these, I still have problems with compile.sh, the problem is :
Building hysplit source library
Building lbfgsb source library
Building exec directory programs
Building the ascii2shp converter
Building the dbf editor
Building the WRF-ARW decoder (requires export NetCDF lib/include)
ERROR


Makefile:7: *** missing separator. Stop.
Makefile:7: *** missing separator. Stop.

Thank you
-Yveete

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