Error When Compile GIZMO

May 15, 2025 by ADMIN 25 views

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Introduction

GIZMO is a highly parallel, adaptive mesh refinement code for cosmological simulations. It is designed to run on a wide range of architectures, from small clusters to large-scale supercomputers. However, during the compilation process, users may encounter errors that can be frustrating to resolve. In this article, we will discuss a common error that occurs when compiling GIZMO and provide a step-by-step guide to resolve it.

Error Message

The error message is as follows:

mpif90 -O3 -Wall main.o accel.o  timestep.o init.o restart.o io.o predict.o global.o begrun.o run.o allvars.o read_ic.o domain.o driftfac.o kicks.o ngb.o compile_time_info.o merge_split.o gravity/forcetree.o gravity/cosmology.o gravity/pm_periodic.o gravity/potential.o gravity/gravtree.o gravity/forcetree_update.o gravity/pm_nonperiodic.o gravity/longrange.o gravity/ags_hsml.o hydro/hydra_master.o hydro/density.o hydro/gradients.o eos/eos.o system/system.o system/allocate.o system/mymalloc.o system/parallel_sort.o system/peano.o system/parallel_sort_special.o system/mpi_util.o structure/twopoint.o  galaxy_sf/sfr_eff.o cooling/cooling.o  -lm -L/home/deng/gizlibs/lib -lz -lhdf5 -g -L/home/deng/gizlibs/lib -L/home/deng/gizlibs/lib -lgsl -lgslcblas -L/home/deng/gizlibs/lib      -o GIZMO
/usr/bin/ld: accel.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: accel.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: timestep.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: timestep.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: init.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: init.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: restart.o:(.bss+0x8): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: restart.o:(.bss+0xc): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: io.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: io.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/bin/ld: predict.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: predict.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: global.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: global.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: begrun.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: begrun.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: run.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: run.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: allvars.o:(.bss+0x8bec): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: allvars.o:(.bss+0x8bf0): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: read_ic.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: read_ic.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: domain.o:(.bss+0x80): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: domain.o:(.bss+0x84): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: driftfac.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: driftfac.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: kicks.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: kicks.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: ngb.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: ngb.o:(.bss+0x4): multiple definition `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: merge_split.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: merge_split.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: gravity/forcetree.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: gravity/forcetree.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: gravity/cosmology.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: gravity/cosmology.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: gravity/pm_periodic.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: gravity/pm_periodic.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: gravity/potential.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: gravity/potential.o:(.bss+0x4): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: gravity/gravtree.o:(.bss+0x20): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: gravity/gravtree.o:(.bss+0x24): multiple definition of `eps_fd'; main.o:(.bss+0x4): first defined here
/usr/bin/ld: gravity/forcetree_update.o:(.bss+0x0): multiple definition of `time_fd'; main.o:(.bss+0x0): first defined here
/usr/bin/ld: gravity/forcet<br/>
# Error when Compile GIZMO
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## Q&A
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### Q: What is the error message indicating?

A: The error message is indicating that there are multiple definitions of the variables `time_fd` and `eps_fd` in the object files being linked together to form the executable.

### Q: What are the possible causes of this error?

A: There are several possible causes of this error:

*   The variables `time_fd` and `eps_fd` are being defined in multiple source files, and the definitions are not being properly removed or hidden.
*   The source files are not being compiled with the correct flags to prevent multiple definitions.
*   The Makefile is not being used correctly to compile the source files.

### Q: How can I resolve this error?

A: To resolve this error, you can try the following:

*   Check the source files to see if the variables `time_fd` and `eps_fd` are being defined in multiple places. If they are, you can remove or hide the definitions to prevent multiple definitions.
*   Check the Makefile to see if the correct flags are being used to compile the source files. You can add the flag `-fPIC` to the compiler command to prevent multiple definitions.
*   Try recompiling the source files with the correct flags and see if the error is resolved.

### Q: What are the possible solutions to this error?

A: There are several possible solutions to this error:

*   Remove or hide the definitions of the variables `time_fd` and `eps_fd` in the source files.
*   Add the flag `-fPIC` to the compiler command in the Makefile to prevent multiple definitions.
*   Use a different compiler or compiler flags to prevent multiple definitions.
*   Use a different Makefile or build system to compile the source files.

### Q: How can I prevent this error from occurring in the future?

A: To prevent this error from occurring in the future, you can:

*   Use a consistent naming convention for variables and functions in the source files.
*   Use a consistent set of compiler flags and options in the Makefile.
*   Use a different compiler or compiler flags to prevent multiple definitions.
*   Use a different Makefile or build system to compile the source files.

### Q: What are the best practices for compiling GIZMO?

A: The best practices for compiling GIZMO are:

*   Use a consistent set of compiler flags and options in the Makefile.
*   Use a consistent naming convention for variables and functions in the source files.
*   Use a different compiler or compiler flags to prevent multiple definitions.
*   Use a different Makefile or build system to compile the source files.
*   Test the compiled executable thoroughly to ensure it is working correctly.

### Q: How can I get help with compiling GIZMO?

A: If you are having trouble compiling GIZMO, you can try the following:

*   Check the GIZMO documentation and user manual for information on compiling the code.
*   Search online for solutions to common compilation errors.
*   Ask for help on online forums or mailing lists dedicated to GIZMO.
*   Contact the GIZMO development team directly for assistance.

## Conclusion
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Compiling GIZMO can be a complex process, and errors can occur due to a variety of reasons. understanding the possible causes of the error and following the best practices for compiling GIZMO, you can resolve the error and successfully compile the code. If you are having trouble compiling GIZMO, don't hesitate to ask for help.